Hmm, memory is a bit fuzzy on the beaming through shields it, thanks. Then again, the answer seems to be 'sometimes'. Kinda like how the Defiant can take on any uber-ship it wants, unless the writers wanna show off a new bad guy, in which case, it gets one-shotted
As for calling the Founders, yeah, obviously too much happening right then and there. Was thinking more once they got away on that one. When the Vorta was going through her 'claim this for the Dominion' speach, I'd have just told her she should check with the Dominion first...
To be fair though only us players know where the fleet came from, ingame everyone probably thinks this is a Dominion invasion as the only evidence from the missing fleet is the empty ships that were recently found which they think might be from that fleet.