Actually it works the totally opposite, the PBX does know when the line is in use. So for example the last one I installed was a simple telecommuter. We added an FXO to a line card port off a Nortel KSU as an extension. The calls come through and are forwarded automatically to the remote worker seemlessly. If they do not answer the call in 4 rings it is then bounced back to the in house voice mail, and secondly if the person is on the line the receptionist can see that from ths busy lamp, same as is an other employee calls from within the office it shows “on another call” on their phones. The FXO gatway does not “pick up” the call until the other end answers. It is more or less passing it through when it goes off hook then makes a connection when the IP phone on the other end picks up. So the remote user also can page the building, do voice calls, transfer calls, conference ETC everything that a user within the building can do. We just supply them with the analog feature commands for the Nortel.
I think I have answered your question in long form ,but simply no you do not loose high level PBX features from what I know at least or have experienced. NOw this is on the QTelNet gateways, I can not speak for other products as I have only used them in lab tests when deciding what product line to carry and these guys won hands down.
If you want to contact me offline I can be reached at dan_c06@yahoo.com