Don't worry about it. When I use apps that use immersive mode, Android shows you a big pop-up telling you to swipe down to get your buttons. It also shows this pop-up during some subsequent startups (not every time, I don't know how often). So really I don't think it's a problem.
I know that people at java-gaming.org won't have problems with handling game with immersive mode
I'd rather know in advance how mysterious such full screen mode is for average user.
I worry in advance because I haven't seen that feature used by any popular android game. Is there a reason for that?