Spelling it germination is a folk entymology
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My mental spellchecker is going wild right now 
etymology: the study of the origin of words and the way in which their meanings have changed throughout history
entomology: the study of insects (branch of zoology)
entymology: the study of ents (branch of tolkienology)
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Some novels always use the large ones for furigana, which is super annoying.
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Oops I misspelled my own joke. I meant entomology, as a pun on folk etymology (replacing unknown parts of words with words that you do know, e.g. spanish cucaracha → misconceived as english cock + roach)
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Some? I actually can’t remember seeing furigana that didn’t do full sized whatchamacallums
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Ents germinate and geminate.
They sssspppeeaakk veerrryyy sslllooowwwly
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Sometimes it’s only hard to see the difference, but there clearly is a difference.
Interestingly, I’ve read that before WWII, furigana was a lot more common in texts intended for adults and it generally used katakana for both furigana and grammar particles etc.
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Katakana is still the norm in legal documents, afaik. It’s kind of a pain.
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Wait, are there any novels that don’t do this?
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Historically, ようおん (digraphs) were indeed written with full-sized kana. So instead of りゃ it used to be りや.
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My copy of 魔女の宅急便 doesn’t. It’s usually not that big of a deal with furigana because if a kanji is glossed as きよう you know it’s not きょう. I’ve definitely gotten confused before though.
I only noticed it for the first time in Kino, so I’m not sure if children’s books differentiate them.
I’ll have to pay more attention in the future!
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Gonna jump in hear and say that, yes, my elementary students in Japan regularly mix up b and d. Also p, g, and q. Also h and n. And ready for this one? They mix up r and v because of the way they’re originally taught to write lower case R. It’s a mess.
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That’s not a problem l and I, that’s a problem with many sans-serif typefaces. And it does cause confusion, especially with names not previously encountered. For example, it took me forever to ascertain for certain that Michael-lan from “Pantheocide” was Michael-lan and not Michael-Ian, and it was only due to the author orthographizing it as “Michael-Lan” a few times.
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Sounds like pretty good preparation for reading handwriting. 
Digression about handwriting...
When I write in my default sloppy cursive, you can’t really tell many t and r apart, some g definitely look like q, x looks like sc, some b look like tr, h could look like t + one stroke from any of u, n, m, etc. Yup, our latin alphabet definitely is confusing. 
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The Japanese class I take has a waiting room with Japanese children’s books in it. I could be wrong, but from what I remember, I’m pretty sure they differentiate the small and large kana in the furigana.
Come to think of it, I’m not sure if they had kanji at all, actually. It seems like the more I try to remember the less I remember.
“Children’s book” is a somewhat broad term. The two books I’d read in particular were 魔女の宅急便 and 時をかける少女. They both uses a limited set of kanji (I would guess the 1000 or so kanji learned in grades 1-6), and all kanji had furigana.
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ツ・ソ are all vertical strokes, like V, and シ・ン are all horizontal strokes, like ＞
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