I have a few other games that detect low vid memory instead of the correct 3GB and they all run fine but the difference with those games is they don't stick a huge error message screen on top of the options screen with no way to exit it.
Totally understand your frustration. Mine is how the text messages in game get cut off at the top of my WS monitor, I've learned to live with the "memory warning" screen since you can adjust all your in game settings by just clicking the icons at the bottom of the GUI screen.
It's important to remember that SFK42 was released in 2008 and no "official" patches were ever done for it. It's a long story but short version is Lighthouse (English publisher) went bankrupt so Graviteam never got paid for SFK42 from these guys, Discus (RU publisher) never paid Graviteam period and holds the rights to SFK42 for a long time. Graviteam did one "unofficial" patch for SFK42 and that was it, everything SFK42 is today was done by the SFK42 community. While SFK42 is very open and just about anything can be modded something's are just hard code and will probably never be fixed like the memory warning and how the in game messages are cut off on some WS monitors.
Cheers