QE can be converted for catapult & trap - it's just that doing it right now is not possible because the detailed design work required to accommodate the systems has not yet been done. Any further delay in the programme for QE will add serious cost, given that large heavily outfitted chunks of the ship are all over the country at the minute, with armies of workers swarming over them.
That does not mean that space and weight in the right place was not allocated - that's relatively easy and it was. The riskiest bit as far as QE is concerned is modifying the power control system software to accommodate the transient loads and harmonics that are likely to be imposed by the EMALS system which is the obvious cat system. While steam is viable, it adds all sorts of risk in terms of legacy systems, design authority, training etc, whereas the EMALS system is currently throwing US aircraft down the runway at Navy Lakehurst. This way the US does a large chunk of derisking for us. I would not concentrate too much on the idea that only one will be fitted for cat n trap. I suspect the plan looks like - complete QE to trial the vessel and systems and spell as LPH, then into reserve for an upgrade to cats, while PoW operates having commissioned with cats. As PoW becomes due a refit, dig out QE and turn about, bit like CVS has operated, but not ideal.
Why did we go to F35C vice B? Well that was another risk reduction exercise. Had we proceeded with STOVL, we were locked into a one-trick pony (ie Dave B or nothing). Before anyone starts up the Harrier II+ or Harrier III argument just think how long and how much it takes to resurrect a production line that has been closed for over 12 years. There's a reason the USMC are buying the GR7/GR9 frames and it ain't because they want to make Call Me Dave happy. By going Dave C, we got away from the single solution (F18E, Rafale, SU33? or even a Sea Tiffy as fallbacks if we're feeling flush and ready to play risk). The USN cannot afford to lose Dave C without ceasing to exist as a force (look at the average age of their frames), but the USMC might be able to live without the fairly risky (RVL anyone?) Dave B.
As for maintenance, the Ark / Eagle debate of the 70s is past. No-one will take a 280m ship into Guzz, endex. However, QE will not fit (length, wl beam or overall beam) into any lock in Pompey, so any docking will need to take place in either Rosyth or if we're desperate Mr Harlands facility in Belfast.