Technically, yes, you can. What you should be asking is "Should I"? Which the answer is no.
Like you've mentioned, since they do call the superclass methods, there is some extra Android OS cleanup magic that happens. It may result in a successful case once in a while, but it's not guaranteed. There is a lot of things that happen in the backround that you don't want to fool with. Don't reinvent the wheel.
If there is code that is ran within the onPause and onStop methods that you would like to use elsewhere, I would create a function called cleanupBluetooth and the onPause and onStop would call and anywhere else it needs to.
If you need to actually call the onPause and onStop methods because you need to stop and halt the activity, you can do that by calling finish() (how to use finish()). The finish() method will call the appropriate Android OS magic that's needed to be called.