I can't speak to the development aspect, as to whether it's highly inefficient to have two projects instead of one. I suppose it is.

Overlap of function seems a common open-source outcome judging from the Maemo media players selection.

Speaking as a user, I don't care that they're separate apps. My use for a stopwatch or countdown timer are so different from my use for a clock or alarm-clock that I'm fine with going to two different apps. There have been times I've found it simpler to have functions in different apps than a single app that does more.

A lot of the pleasure in FlipClock is aesthetic. You could give it a different look for a stopwatch/timer, but the primary theme doesn't seem very apropos. For the stopwatch/timer, I'd prefer great simplicity.

Finally, they're developing specifically for Maemo 5; and, fortunately, you haven't abandoned us Maemo 4 Luddites.