Yes, that would definitely be an issue in calculating game times accurately and consistently. Even Steam struggles with that sometimes, though, so it wouldn't need to be 100% perfect. It's still a challenge, though, of course.
In rudimentary form, it's really not that difficult to detect when a game opens and closes, but there are some bad caveats, and we'd have to make some assumptions that would likely be broken here and there. For example, if you loaded up Retroarch to play Super Mario Bros., but then loaded a different ROM from inside of Retroarch instead of exiting back out to LaunchBox, the time would be reported incorrectly. There's lots of other potential related issues as well, such as some games using a launcher EXE; that would pretty much break the feature for that game.
That said, it may be time to implement this soon, regardless, at least in rudimentary form. I honestly don't think it would be worth the time and effort to integrate with every single game, emulator, etc. in order to do it properly, but it wouldn't be that difficult to do it generically, even though it would probably be fairly inaccurate.