Am I allowed to do this?
Yes, you are. But...
You knew there was going to be a but, didn't you?
What gets compiled and linked? Only the sketch and any source files referenced by including headers in the main sketch.
If you have a class TimerWrapper that includes TimerOne, and a sketch that includes only TimerWrapper, the sketch and TimerWrapper will be compiled, but TimerOne will not be. Any references in TimerWrapper to functions in TimerOne will result in undefined external references, as you are seeing.
The solution, then, is to include TimerOne.h in the sketch, too.