Haleivi:
1)I’m not sure that your understanding of R’ Meir is correct. All the Gemara says is that R’ Meir argues. Then it says shene’emar… and quotes a pasuk which proves that Rasha V’tov Lo can defy explanation. I don’t think that necessarily means that R’ Meir was only arguing about Rasha v’tov lo. It could be that that pasuk was just used to prove that Moshe’s request to understand H’s ways was not answered, the proof being that Rasha v’tov lo is unexplainable. I am not saying that you are wrong (in fact I think I am more noteh to your reading) but I am suggesting another reading.
2)As for the Ramban, he discusses tzadik v’ra lo in his introduction to Iyov. He does not directly mention the Gemara in Berachos but he doesn’t seem to accept the Gemara’s answer of “tzadik gamur…” as the final word on the matter – he points out that there can be tzadikim gemurim like Iyov who still have troubles.
3)As for Rabbeinu Yonah, he is explaining pshat in the Mishnah in Avos which by the way, Rashi explains pretty much the same way. He also quotes the Prophet Jeremiah so he seems to have good backing. Additionally, his understanding of the Gemara in Berachos might be in accordance with what I wrote in point#1 or point#2.
4)I won’t claim to be an expert in Maimonidean thought, but in Moreh Nevuchim 3:17 he discusses different views of Hashgacha and he seems to hold that any little thing that goes wrong for someone is a punishment for some bad deed and every little thing that goes right is a reward for a good deed. He implies that Yissurin shel ahava is a minority view (and again implies it in 3:25).
If one believes in Olam Haba and/or yissurin shel ahava, I don’t really see why anyone would have the kashya of tzadik v’ra lo. But anyway my original point was that if tzadik v’ra lo makes perfect sense based on the concept of gilgul, then anyone who struggled with this issue perforce did not know of/hold of gilgul. Now perhaps you can make the same argument in regards to olam haba/yissurin shel ahava in which case I would either be stumped or I would say that perhaps they hold like the Rambam (or what I think the Rambam seems to be saying).
In summation, this is definitely a complex topic and I am definitely not claiming to have expertise in it.