If you add さん, I don’t think it means you are referring to a specific person, it’s the shop, restaurant, company etc you are talking about.
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Yeah, I just got it from here where the example would be referring to a baker as パン屋さん, which actually showed up in the Microsoft IME suggestions when I typed in パン屋!
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I think this is rather 変わる (to change). So: His love for plants does not change.
Note that the verb is not in potential form (that would be 変わ れ ません), so it cannot be “cannot” like you translated.
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Yes I think you’re right. Thanks! There seemed to be multiple possible choices and then I overthought it. I forgot about the potential form entirely! 
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The text you linked says it’s not only for persons but also for entities. And I’m not sure Japanese people would interpret these expressions as something like „Mr Shop“. 
I doubt it really translates well at all. I don’t think I’d walk into any store and address the person working by their job title.
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p. 141
家では、おばあさんが買ってくれた植物の本が、宝物。
At home, the books on plants that his grandmother bought him, were a treasure.
図を見たり、写したりしていると、時間が経つのも忘れてしまいます。
When he looked at the diagrams or copied them, he ended up in forgetting the passing time.
山にでかけ、珍しい草花を集めては、本で調べたり、周りの人に名前を聞いたりするのです。
He went out in the mountains, collected rare flowering plants, and looked them up in his books or asked the people in the surroundings for their names.
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pg. 141
家では、おばあさんが買ってくれた植物の本が、宝物。
At home, a book about plants bought for him by his grandmother was a prized possession.
図を見たり、写したりしていると、時間が経つのも忘れてしまいます。
If he was doing things like looking at or tracing the pictures, he would forget about the passage of time.
山に出かけ、珍しい草花を集めては、本で調べたり、周りの人に名前を聞いたりするのです。
Going out to the mountains, whenever he collected unusual flowers he would look them up in the book and ask surrounding people their names.
The final sentence tripped me up slightly. I’m used to 聞く meaning “to hear”, but that didn’t seem to work as well.
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Yes, that’s a bit tricky. In books geared towards adults, the meaning of „to inquire“ is often expressed with 訊く which clarifies things a lot. But in children’s books you generally won’t find this kanji.
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In this book it was just written in hiragana, so the meaning had to be entirely guessed from context. Back when I first started studying Japanese I never imagined that more kanji would make reading easier! 
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Oh I see - I don‘t own the book and only lurk in this thread as you can probably tell by now 
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Page 141. I feel like this page was on shorter and easier side of things.
家では、おばあさんが買ってくれた植物の本が、宝物。
At home, his prized possessions were books about plants that his grandmother was buying for him.
図を見たり、写したりしていると、時間が経つのも忘れてしまいます。
While looking at diagrams, tracing images, he was totally forgetting about time passing.
山に出かけ、めずらしい草花を集めては、本で調べたり，周りの人に名前を聞いたりするのです。
Going to mountains, he was gathering rare flowers, and look up them in his books, and asked people around him about their names.
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There’s a small typo here: It’s supposed to be 見たり 
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p. 142
「それは、内の田舎では、ビルムシロと言いますよ。」
“That is called a ‘birumushiro’ in our countryside.”
「本には、ヒルムシロと出てリるよ。
“In the book it is listed as ‘hirumushiro’. (pondweed)
場所によって、言い方が違うのか。ふうん、面白なあ。」
Is the way of saying different depending on the place? Hmm, that’s interesting.”
やがて、大きくなった富太郎は、東京で植物の研究をしている先生たちに、会いました。
Finally, in Tokyo, the grownup Tomitaro met teachers who were doing research on plants.
先生たちは、田舎から出てきた富太郎が、たくさんの植物を自分で集めていることに驚きました。
The teachers were surprised that Tomitaro, who came from the countryside, had himself collected a log of plants.
そして、「牧野さん、一緒に日本の植物のことを調べましょう。」と、励ましてくれました。
And they encouraged him: “Mr. Makino, let’s investigate Japan’s plants together.”
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Page 142
『それは、うちの田舎では、ビルムシロと言いますよ。」
“That, in our contryside, is called birumushiro.”
「本には、ヒルムシロと出ているよ。場所によって、言い方が違うのか。不運、面白いなあ。」
“In the book, it is listed as hiromushiro (Potamogeton). Because of dialect differences, right. Bad luck, fascinating…”
やがて、大きくなった富太郎は、東京で植物の研究のしている先生たちに、会いました
Before long, grown-up Tomitarou was meeting with professors who were doing plant research in Tokyo.
先生達は、田舎から出てきた富太郎が、たくさんの植物を自分で集めていることに驚きました。
These researches were especially surprised by how many plants Tomitarou, who was from rural area, collected himself.
そして、「牧野さん、一緒に日本の植物の事を調べましょう。」と、励ましてくれました。
Thus, they encouraged him: “Makino-san, let’s study japanese plants together!”
This sentence
先生達は、田舎から出てきた富太郎が、たくさんの植物を自分で集めていることに驚きました。
I could not parse satisfactory. Namely the final verb 驚きました, based on context, should be done by 先生達 which are topic:
As for professors, they were surprised…
On the other hand, we have 富太郎が marked as subject - is he a subject of sub clause?
And small confirmation if I’m correct, in the last sentence:
そして、「牧野さん、一緒に日本の植物の事を調べましょう。」と、励ましてくれました。
the final verb is again grammar point てくれる “do something for someone”. Hard to incorpoorate into English translation anyway.
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I translated ふうん= 不運 “bad luck” out of respect to long vs short vowels, and I agree it does not make sense at all, while short ふん is just “hmm” and fits much better. 
I read this with the same meaning as you. Maybe someone will have a real answer but it seems to make sense that there wouldn’t be two は in the sentence, and so the topic of the sentence as a whole is the researchers surprise while が just marks Tomitarou as the subject of the sub clause.
It’s a bit funny, since in English it’d sound OK to say something like “what they said was encouraging for him”, or “what they said was encouragement for him”, but not really “they encouraged for him”.
Maybe and they said “Makino, let’s study Japanese plants together!”, which was encouraging for him.
I keep reading Makino’s name as ぼくや and it’s annoying.
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pg. 142
「それは、うちの田舎では、ビルムシロと言いますよ。」
“This one in the countryside is called ‘birumushiro’ (a pondweed).”
「本には、ヒルムシロと出ているよ。
“In the book, it appears as ‘hirumushiro’.
場所によって、言い方が違うのか。
According to the location, the way of saying it changes?
ふうん、面白いなあ。」
Hmm, how interesting.”
やがて、大きくなった富太郎は、東京で植物の研究をしている先生たちに、会いました。
Eventually, a grown-up Tomitarou met teachers researching plants in Tokyo.
先生たちは、田舎から出てきた富太郎が、たくさんの植物を自分で集めていることに驚きました。
The teachers were astonished that Tomitarou, coming and going from the country, was collecting so many plants himself.
そして、「牧野さん、いっしょに日本の植物のことを調べましょう。」と励ましてくれました。
And then, “Makino, let’s investigate Japanese plants together.” they encouraged him.
Just like yesterday with 聞く, today I was a bit thrown off by multiple definitions of 出る. And there are many. In sentence 2 I translated it as “appears”, but I’m not so sure.
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Yes, he is the subject of the subclause (the part from the comma to 集めている). 
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