The problem, ultimately, is that the Polish-Lithuanian Commonwealth was dominated by Poland, and said Polish nobility was not interested in treating religious minorities equally, as GDL did. Republic or not doesn't matter here - republics can quite easily become tyrannies of the majority. There's a reason why there were so many uprisings on the territory that is Ukraine today, back when it was a part of the Commonwealth:
It changed with time, but the Polish nobility wasn't the ones persecuting religious minorities for the most part.
For one thing nobles took a lot of Jewish immigrants, used them as middle management (which frustrated the church, who in turn sent angry peasant mobs against Jews, which meant Jews had to work with nobility for their protection).
Also a lot of nobles weren't Catholic, especially in 1500s protestantism was very popular (about 1/3rd of nobles and majority of magnates were protestant). Only in times of Zygmunt 3 Waza who was super Catholic and introduced some discrimination it changed significantly.
Majority of nobles from eastern parts of PLC were orthodox at first (later they polonized and switched to Catholicism mostly), and there were some Jewish and Muslim nobles (but it was very rare). They still had all the rights including voting for kings, wars and taxes.
> There's a reason why there were so many uprisings on the territory that is Ukraine today, back when it was a part of the Commonwealth
Mostly economic, but yes, there has been some religious persecution there. Especially after the attempts to create orthodox-style pope-sanctioned religion in Ukraine.
The Orthodox nobility had the same rights at first. But, as you say yourself, almost all of them have switched to Catholicism over time. And the reason for that was that it was the only way to preserve both the rights and the social standing in the long term.
As for nobles not carrying out religious persecution, I don't even know what to say. Local magnates were the main drivers of the religious persecution of Orthodox Ukrainians and Belarusians. And sure, that persecution was often economic in nature, but it was also very clearly carried out along religious lines.
I'll grant you that religious intolerance in Poland was primarily between Catholics and Orthodox, rather than Catholics and Protestants as elsewhere in Europe. But that's to be expected from a country where most subjects are either Catholic or Orthodox, no?
EDIT: I suppose our perspectives are so different because we're focusing on different time periods. My take on this is that early Polish-Lithuanian Commonwealth inherited many of the political arrangements of GDL, and tolerance was one of them. But as the center of political power shifted over to Poland over time, they were weakened.
https://en.wikipedia.org/wiki/Cossack_uprisings