I just recently tried using the BDM bypass, so I can't compare to the older version of BDM. Currently running BDM 220.127.116.11 and BES 18.104.22.168.
However, once I'm connected via BDM, (I even turned off wireless), I can do everything via the BDM. No restrictions that I've noticed so far.
The only difficulty I had was our bes is named
l which was not a valid FQDN within our dns. I hadd to add a user defined router.
to get it to communicate with the bes correctly.
I have connected both carrier and the wifi blackberry through the BDM to the bes.