I think the reason why they decided against it was because of the traffic that has to be stopped whilst the TPE’s from the airport have to cross over. As it currently stands they only have to use the slow lines and don’t affect the fast or the eastern lines.I notice no one seems to have mentioned the line that turned left almost IMMEDIATELY out of Piccadilly, just before Ardwick Station. The viaduct remains and is clearly visible on Google Maps (satellite view) along what is appropriately called Viaduct Street. However, this would not remove the need to reverse out of Victoria for Leeds as it joined the Philips Park Line just north of the A635 (Ashton Old Road) and entered Victoria westbound.
It would have made more sense to use that viaduct as the disruption would have been a lot less.
If it didn’t call at Victoria then it could go straight to Leeds via Huddersfield or the Calder valley.