I think it's pretty clear that any kind of boarding operation would entail scrambling, webbing, neuting the ship out, possibly deliberately damaging navigational and thruster systems (depending on how intact of a state you care to recover the ship in) before you board it.
The real question in my opinion is how would shields and/or hardened armor surfaces interact with a boarding pod? Surely shields would have to be battered down first so that the boarding pod can actually make contact with the hull of the ship, but what would happen if shield integrity was momentarily re-stablished mid-boarding? Also, what about hardened armor surfaces - the boarding vessels would have to carry some fairly significant cutting equipment, on scale with much higher-power, weapons-grade systems, otherwise cutting through the armor could take hours.