One of the principal issues with TPE is that it has previously made (in my opinion quote ludicrous) agreements with ASLEF regarding what is called "more important work". In simple terms this means that drivers diagrams (what trains they drive each day) can't be altered from the base long term plan agreed with the unions, which matches the normal published timetable, unless for very specific reasons - even on the day itself. "Staff shortages / uncovered duties" are not one of these specific reasons.
So even if the driver's start and finish times remain the same, and don't alter, TPE cannot alter the content of their duty on the day to cover for staff shortages elsewhere - i.e. they cannot shuffle drivers around to cover as much as possible. Now admittedly many drivers will help out, but many won't, and thus the company will assume the worst and just cancel trains the evening before to avoid a last minute cancellation on the day if the driver refuses to do something different inside his working hours.
Combine this with the equally ludicrous way that the company has planned it's work allocations to depots and has planned things to often have multiple crew changes along the length of many services, then we have the chaos everyone now experiences.
Irrespective of how many qualified drivers you have there is always a need for some overtime and flexibility short notice, so until such time as the "more important work" rule is tackled, or rest day working returns, then things will still stay a mess.
The fact the Sunday timetable remains reduced when there is no Conductor industrial action at all, and seemingly plenty of staff available to work on Sundays in some locations, is obviously part of a wider plan to either punish staff and deny overtime or reduce the timetable in the medium to long term and reduce passenger expectations (and thus save wages in the long term) or another ploy to pit passengers against staff so the Government can steam in with some radical proposals to "break the unions" and modernise the workforce- which is their stated aim.