If you use Territory Management data structures or functions, your package might become dependent on this feature to be active in the Orgs where users are going to install it. This might reduce the acceptance of your package for those who can't activate it or don't like it.
The supervisor/rep scenario sounds pretty easy and should be no problem. TM also introduces a second hierarchy parallel to your current Role Hierarchy, so you cand model the assignments independently.
Mind that there are two different versions of Territory Management which are coupled to a corresponding version of Forecasting.
It doesn't mean you need to activate Forecasting but your Forecasting will be limited to the respective version. This means the other way round that Organizations with Customizable Forecast and currently no TM can't simply turn on ETM 2.0 but only TM 1.0
Using dynamic APEX and SOQL you might also be able to avoid a system-enforced dependency and write code which works dynamically with both versions of TM or even with a custom TM-substitute or completely without. This will result in more effort for development but will bring the most flexible solution. If possible I would try this approach.