I have the console enabled in Doom 3 so that I can set the FOV to something higher (because the default FOV is crap).

Every time I do something that would have given me an achievement, I get a popup that tells me achievements are disabled because the console is enabled.

I don't care about achievements, I just want the popups to stop. They don't go away unless I use a controller or press enter.

Every time it happens, it's like a slap in the face.

NOTE:

I know I could disable the popup by disabling the console, but I want the console. That's the only thing that makes the game playable.

Well since you don't care about achievments what about this

https://www.moddb.com/mods/classic-rbdoom-3-bfg-edition

I tried it, but it wouldn't run. It requires directx 10 and Windows 7. I'm still using Windows XP.

That's probably the only simple solution though.

Possibly because of FFMPEG since it uses the same version of directx.
I guess I was using the xptools on MSVC for no reason then :(

I did not tried this with specifically DOOM3 ports but with few other NT6 API-targeted games unofficial One-Core API compatibility layer for XP helped very well. Even for x64 release of the OS.
It conflicts with XP's East asian languages support, though. This support must be uninstalled to avoid run-time errors in comctl32.dll.

Settings > Features > Uncheck the box labelled achievements.