Yeah, unfortunately the Kotor Patch Manager needs a clean executable (you can use a gog one or the editable exe, both work), the best way to get widescreen support back in that scenario is to use @J's https://github.com/J0-o/KotorUniResPatch patches.
They work quite well, but depending on what you already have installed you may need to undo existing overrides in order for everything to look right. (e.g. the high resolution menu mods) They've properly scaled pretty much every interface in the game to look right (and even unlocked the in game resolution menu)
This does have me thinking that it might be a good idea to have a standalone version of this mod that can be dropped in to existing modbuild installs or installs with other pre-patched executables. Stay tuned for something on that, I'll see if I can take a look at what is needed on the weekend.
I have this same issue, after some basic testing I found using uniws to fix the resolution makes the kotor executable into an unknown so the patches dont work.
I'm playing now using this, and my companion has power attack 3, and critical strike 1. I figured they'd alternate uses of thing, but instead they're just spamming critical strike 1. O_o