I think most people travelling from Piccadilly to Leeds will continue to take the first departure, regardless of whether it is a "fast" via Oxford Road, the Ordsall Chord and Victoria, or a semi-fast via Guide Bridge. Likewise travellers from Leeds to Piccadilly.
Piccadilly, not Victoria, will still be Manchester's main hub and the fasts will not be able to overtake the semi-fasts. So I think the semi-fasts will carry a lot of end to end passengers. Travellers between Piccadilly and Selby/Hull will certainly not change at Leeds.
The TPE franchise agreement does not require the semi-fasts to stop at Guide Bridge.
That doesn't mean they cannot stop at Guide Bridge...
And how do you know that? Have you seen a draft timetable? It's perfectly possible that these services will be overtaken. It may even be desirable.
Admittedly only two of the fasts will use Piccadilly. But that still doesn't mean that they won't be overtaken by going via Victoria.
As for the Advance issue, TP advances are typically quite expensive, and they are far more likely to use their yield management to encourage people to use the 5 car non-stop services, rather than the potential 3 car stopping service.
but actually - that's exactly what is needed. I'm very nervous about the forthcoming trains - they look really nice for long journeys but I do think the Huddersfield and Leeds dwell times may be extended with a lot of pushing and shoving as passengers board.