The Baldur's Gate 4-in-1 retail box / compilation you have linked first definitely works with the mods, it's just the Gamersgate version specifically I remember reading warnings about when it last went on sale.
The BG:Enhanced Edition actually comes already modded in some sense, it's updated to be using the latest BG2:ToB engine (like TuTu does), and already optimized even better for widescreen gameplay (like the widescreen mod, but better), as well as other minor graphic rendering enhancements which should eliminate the directdraw slowdown / shadowing trouble. So while the warning is somewhat true there, I don't think BG:EE is really meant to run with mods in the same way you'd want the original release to use them.
The extra content exclusive to BG:EE will probably make it incompatible with Baldur's Gate Trilogy, if you prefer rolling that way (as I do). This is just a guess, though.