Hm, so two issues. Relative clause <> embedded clause. When I say relative I mean only those that modify a noun. And also, sorry I wrote that too fast; it’s actually only available when there is no object in the relative. 
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That’s not a relative clause.
A relative clause would be:
俺の食べたもの
The thing I ate.
おまえの食ったもんは犬の餌だったんじゃねーか！
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Oops, sorry, somehow skipped over the “relative” part in your post, since originally we were talking about an embedded one. Thank you both for clarifying!
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At first I thought this was an explanation before I realized you were asking a question, because it seems like you understand it perfectly well. You can’t change が to の in the situation you described for exactly the reasons you pointed out. If you have the DBJG the section on relative clauses points this out with a similar example:
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An interesting mnemonic is that it’s quite similar to how, when English turns a sentence into a gerund, the subject takes the genitive marker (either a specific pronoun or 's): I eat => my eating.
Just to add to this, AFAIK, the restriction is larger and seems to apply to all objects, even if they are placed before the subject.
Sources...
For example, I just pulled this from the abstract of a chapter of the Oxford Handbook of Japanese Linguistics:
It also describes the transitivity restriction on the GNC, which prohibits co-occurrence of an accusative DP with the genitive DP
And, from a paper (Ochi, Masao. 2005. “GA-NO conversion and overt object shift in Japanese”) I just picked straight from Google, this precise scenario is discussed:
As Watanabe (1996) points out, the saving effect observed in (4b) should not be framed in terms of an adjacency requirement imposed on genitive subject and a predicate of the prenominal clause, since preposing of a direct object does not lead to improvement, as shown in (5b).
(5) b. *Hon-o Taro-no katta mise
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I like that!
Sounds like a mathematician wrote this. But then again, I guess linguists are the mathematicians of languages…
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You know how in English we might say something like blah blah blah, right?". You’re kind of making an assertion but that “Right?” at the end makes it sound less forceful and gives the other person more room to disagree or give their opinion. How do you do that in Japanese?
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Wouldn’t that be でしょう or ね?
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I think ね is only when you’re soliciting confirmation though. I’m looking for more of a less forceful assertion. Like when I think something is true, but I don’t want to come off as rude by being too direct about how right I think I am. Like this.
“Amy’s collar was blue”
“Amy’s collar was blue wasn’t it?” or “Amy’s collar was blue right?”. (shows a little more uncertainty)
Checked the dictionary. It’s probably that one. How do people tell the difference between the “it seems” でしょう and the “Right?” でしょう.
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intonation is different. don’t ask me how 
. you’ll probably learn it through context and repeatedly hearing it in the wild
Wow, I actually did not know よね meant that. I hear it and see it all the time but I thought it just meant ね but with more “oomph” ya know?
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The latter would likely be accompanied with a rising intonation.
I’ve noticed that verbs ending in ~す are usually transitive and verbs ending in ~る are usually intransitive. Moreover, I’ve also noticed that verbs ending in ~げる are transitive and verbs ending in ~がる are intransitive. Why is this? Is there any underlying reason for this, or is it mere coincidence?
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From here:
Yep. You guessed right. So you shouldn’t be too surprised to learn that the First Law of Japanese Transitivity is:
All verbs ending in す su are transitive verbs. Whether they have an intransitive “pair” or not.
Su-ending verbs are based in suru . They are transitive.
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There’s always an underlying reason. Usually it’s etymology. 
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Though, frustratingly, when する attaches to a noun, you can’t really tell at all if the resulting word will be transitive or intransitive. I think that ends up being more challenging than the various pairs, since there are patterns you can learn with those.
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I’m currently learning 何千 (“thousands”).
There is an example sentence, which translates to “Suddenly, thousands of bacon strips fell from the sky.”.
It goes like this: とつぜん、何千ものベーコンがそらからふってきた。
What is the purpose of もの here? Why not just 何千のベーコン?
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It’s definition #3 here, used to emphasize amounts. Not using it would sound more “matter of fact.”
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