[Graphics] OWs sharing the same palette

So, because I found out what did I do wrong with my protagonist's facing wrong direction problem it created another issue. In order to keep pop ups (exclamation mark, ^_^, etc. ) and surfing OW untouched I need to give them a different palette but it seems, that hero's palette and palette of graphics I want unchanged are connected and I can't find a way to separete them. Is there a solution for that?

Side note: Overworld Manager has turned my ROM into trash, even without changes done to my ROM.
I've also patched my ROM with Navenatox's patch.

The default palette used by the player OWs and the exclamation pop ups are connected yeah, not sure of a way to de-link them binary-wise. Are you not able to give your player characters a different palette than the one used by default, for example, one of the ones used by NPCs so that you can leave the default one alone? I remember having done that in FR without any issues a few years ago. Then again, not sure what kind of difference the palette patch makes to that or what kind of effect that might have since that was before that patch existed.

Side note: I would really avoid OWM for this reason, I've never used it myself but a lot of people have reported issues with it and relying on a tool to repoint things like the OW table is more often than not dodgy.

If you are using Fire Red then you can use Dynamic Palette Patch.