That Qt manages the main loop shouldn't be a problem - indeed, there are arguments in favour of this, for example it means the API/OS can manage better for battery life, rather than having to trust the programmer to get that right, which is important for mobile use. Why do you need control of the main loop?
It is a problem for a real-time game if due to the Qt main loop & timer event implementation one cannot get a stable framerate at all. I'm clb's co-worker and thus have worked with the Tundra codebase as well, and there has been a problem with implementing a sensible frame limiting mechanism using Qt. Either one uses a non-zero timer period, in which case the application may sleep unnecessary extra time, or use a zero timer period, in which case the main loop runs as fast as possible, but there is the risk of the application actually choking on OS window messages. The "extra sleep" problem is actually worse in Qt 4.8, and partially due to that we rolled back to Qt 4.7.