I'm aware that IDs can be done in the mode itself but if there's no way of monitoring the ID I'm sure the FCC would take a dim view of it.
After all what's the point of an ID if there is no ready method to observe it? Shouldn't be a problem though if there's going to be a CW ID in the software.
Going back to Andy's point, during long Pactor message transfers (like a WX fax) does the Winlink software ID every 10 minutes for both the RMS and client? I always assumed it did but now I'm not sure.
I'm fairly sure it does in WinMOR.