I’m asking anyone to please investigate this and help figure out why this is and if it can be fixed (The GOG version running just as well as the Steam and DVD version)
Interesting. I also experienced the long loading times but I was sure it's tied to hardware problems. There's one level where I experienced particularly long loading times, it's the first bossfight against the Necrogiant - and this fight also features some graphics corruption on my system. Gotta check whether my CD release behaves differently.
And no, I'm not making a mistake here: the Polish version of the original Painkiller was actually released on 2 CDs featuring low resolution cutscenes. :P