You can ask at check-in but IB is not known to accommodate such requests. So rather unlikely. As I recall it, you have to pick-up the bags at BOG and clear customs anyway, so not much gained if IB would agree to tag bags to MDE (admittedly, I might not be updated on whether you have to collect the bag(s) and recheck at BOG even if tagged to MDE).

As for your return flights, it is also rather unlikely that AV will tag bags to final destination. You can ask but expect a "No". Anyway, not the end of the world. You pick-up the luggage at the luggage belts from domestic flights at BOG and proceed upstairs to check-in with IB. At most it will take 10-15min longer than if you do not have to collect the bags at BOG.

Again 3 hours at BOG is plenty of time and nothing to worry about.