Yes, the original intention (as I understand it) was that GW-ATP and ETCS would be able to operate side-by-side. I believe this was actually tested and found to be the case ---- but for whatever reason, while it might be the case on ideal test trains, it's not the case on 345s. From what I gather it's the 345s themselves that are considered "at fault" for this --- but I don't know enough about the radio frequencies involved to be able to form my own opinion on who is really at fault here. But you'd have thought they'd have had some radio engineers to confirm whether GW-ATP and ETCS would be able to theoretically run side-by-side or not, so I would imagine as a result that the "problem" item here is the 345s being unable to sufficiently discriminate the ETCS from the GW-ATP signals.
From the sounds of it, it seems that they've decided that rather than do the "correct" thing and make the 345s better at discriminating between the two competing signals, it would instead be simply easier to wait until the GW-ATP is gone and then have the 345s running on the ETCS alone. But this would require either a problematic transitionary period where you can have one or the other but not both systems running, or an intermediary period where they set up something like TPWS+ only to abandon it once ETCS is working. Neither is particularly a great option...