I get the feeling that this 'commercialisation' option will mean that once the ships have been built & are handed over to the RN, that they will then spend 2 - 3 years finding 'faults / problems' & spending more taxpayers money to change things. Military regulations & the likes of ANEP 77 will swing a heavy hammer blow on some of the things you mentioned. Commercial ships are built to a price point, Military / Naval vessels are usually built to more stringent rules, as when the brown smelly stuff hits the round rotating thing during action stations, you want the kit to work.
I know that RFA vessels that I've worked on over the years are usually built to commercial standards, but again, the areas that need 'marinisation' are usually addressed during design & on the odd occasion that something comes outta the woodwork (like an incompatible system / issues with electrical signal harmonics / interference, due to incorrect / lack of cable segregation), these issues have to be fixed.