Here's a pretty good (and long) YouTube video of someone making comparisons:

- between PS1 version vs PC GOG version

- between original PC version vs PC GOG version

Breath of Fire IV Updated PC Port! First Impressions & Comparison

https://www.youtube.com/watch?v=cpbO8pL7ba4

Though it's a few days old, so much of the hotfixes won't be part of it. But some of the top issues are mentioned.

The video is a side by side comparison, though not always synced.

The video mostly compares other versions to the GOG version with Point sampled (3rd party, since video was done before hotfix) option.
.