Do you have a source for these statements?
It's hard to qualify personal statements without a source. Is it the designers talking or an author's interpretation?
The quote you mention was Professor Louis Rydill, the CVA-01 project leader 1962-67, not a chief designer. His remark referred to the fact that the design incorporated so many innovations that could potentially lead to delays and cost overruns while having an under-resourced and short staffed team to deal with all the issues.
Since size and cost were critical factors it is not surprising that compromises had to be made.
Compared to previous carriers CVA-01 traded armour weight for structure weight for increased volume. Ratio of volume to displacement was 4.1, Centaur/Eagle were around 3.2 and the later Invincible 4.6. Yet by contrast CVA-01s structure weight was greater than Eagles. The use of QT35 steel (developed for the SSN programme) was cut from 9,000 tons to 3,000 tons to reduce the costs by £2.5mil and ease the problems of too few trained welders in the industry. The QT35 mainly remained in the armoured and high stress areas and older QT28 and B quality steel substituted. It was estimated this reduced the splinter protection resistance by 7%.
For an in-depth coverage of CVA-01s construction and the various steels used I would recommend Ian Sturton's article in Wrship 2014
The hangar was 96% of Eagle's by area so was quite tight but probably the biggest possible given the restraints on the hull size. Crew accomodation was to the standards of the time with space for additional personnel over that required for the war complement with air conditioning to tropical standards.
Armour was splinter protection only, generally provided by the structure of the ship (1.0-1.25in thickness) which protected against splinters from 500lb MC bombs and shells up to 4.5in calibre with some reinforcements in certain areas. The operations compartments had 1.5in top and side plating to keep out 6in shells. The weapon magazines were protected against splinters from 1,000-2,000lb Soviet ASM warheads exploding outside and 6in AP shells, 1,000lb MC bombs and 60lb SAP rockets. A large missile could penetrate the magazines and topsides penetration could not be prevented but sub-division, fire-fighting gear and shock protection would lesser the effects. Nuclear blast pressure of 10psi could be withstood to enable the ship still to be able to steam. The flight deck could withstand 3.5psi to remain operational with her airgroup.
The 19ft thick torpedo defense system was quite effective, defeating a 1,800lb warhead with protection up to 1,500lb at the ends. The then biggest known torpedo warhead was 1,200lb.