It's not mandatory to lodge the transmission application electronically. Without having lodged a TA via PEXA; yes, I believe you should be able to lodge the Transmission Application via PEXA if you have the paper CT however if the CT does not have a CAC on it you may need to produce it at LRS and get an E-Transaction Production Number.
Thanks Emma. Another question, which flows on from this discussion and which occurred to me this evening as I was preparing a client authorisation form in an unrelated matter, and that question is - has the client authorisation form been updated to include a TA? I suppose, having looked at the form again, the TA comes under the heading 'other'; something for when TA lodgment in PEXA becomes mandatory, perhaps?