So I downloaded the new installer for fallout 2 and it comes with sfall 3.2a pre installed. Can I use unofficial patches (like Fallout 2 patch 1.5 for example) with it? I really think the game shouldn't come with mods preinstalled and instead come with said mods and instructions for them in goodies.

I agree with you. I'd rather it come in it's original state and let me decide what, if any, patches/mods I want installed. GOG pulled a similar stunt a while back by including a version of sfall, which caused some graphical glitches making it unplayable for many. I'm glad I still have my original download from way back when I purchased it in 2008.