I play SOG with other mods at all times. In fact in one of my Modlists, mainly used for screenshot purposes I also run large mods such as CUP, CWR3, RHS AFRF and many others without any issues.
I agree that the main menu change wasn't ideal but I'm usually only on the main menu for a few moments before I'm into the editor so it doesn't effect me particularly.
I haven't looked at the compatibility data but we saw similar things with ArmA II's Lite versions of the PMC and BAF DLC's. The idea isn't to charge you for content you could have for free but rather to ensure that no members og a group are excluded from sessions if they can't afford the DLC at that time.