So in any reconstruction, in order to achieve a full length hangar clear of the boiler uptakes, it seems to me that the floor of the lower hangar must be raised by one deck, to the level of the quarterdeck. That creates a vacant space under the new hangar floor that I referred to previously. BUT the forward extension of the new hangar then removes two decks worth of space forward of the boiler uptakes.
The available documents for the Implacable reconstruction are infuriating for their apparent randomness and incompleteness, to the point it is impossible to say for sure what the planned £10.5million modernisation was when it was formally abandoned in June 1952. However, I am confident that your point above about the location of the hangar deck is correct. The story itself is perhaps a bit more convoluted though:
Late in 1950 DNC investigated reconstructing Implacable "similarly to Victorious but with an additional deck under the hangar". This would have required a 7ft 6" bulge giving the ship a 110ft beam and a deep displacement of 36,000tons. The real driver for this was a desire for a side lift forward on the port side, though it also created significant benefits in terms of internal volume. With the additional deck the freeboard to the hangar deck would have been 23ft 6" and total depth would have been 80ft (compared to 72ft in Victorious and 86ft 2" in Ark Royal).
This approach never made its way into the draft staff requirement and probably died about August 1951. DNC viewed adding so much weight to a supposedly quite lightly built hull undesirable and at 110ft beam the only UK naval docks she would be able to use were Devonport No.10 (which she was programmed to be reconstructed in) and AFD.XI then at Portsmouth. Additionally, such a rebuild would take longer and be more costly. I have a hypothesis, for which I have no direct evidence, that DNC would also have been motivated to keep the Implacable reconstruction as identical to the Indefatigable reconstruction as possible to reduce the workload on his overworked department. Indefatigable was to follow Victorious at Portsmouth so it wouldn't have been possible to make her so large, e.g. she would have been a separate design effort if Implacable was given a 110ft beam.
Implacable's pre-reconstruction depth was 71ft versus 72ft then planned for the reconstructed Victorious. Maintaining this whilst giving Implacable the same number of decks as the reconstructed Victorious would have left 6" less headroom under the beams on the upper gallery deck compared to Victorious, which was considered undesirable. The ideal approach was to increase Implacable's depth by 6"-1ft making overall depth almost identical to Victorious. Essentially the agreed approach was probably to turn Implacable into a longer, four shaft, version of the reconstructed Victorious. I say probably because that's the best I can manage based on the documents actually available.
The extra deck approach is a fascinating what-if. With a side lift, putting aside the issues with this in Ark Royal and Hermes, she could have carried a larger air wing than Victorious and it may have been possible to extend her catapult runs in later refits to accommodate heavier aircraft. It was also intended, at least initially, to re-boiler her so she would have had the same superior steam conditions as did the IRL Victorious. Her reconstruction at Devonport could have been done instead of Centaur, avoiding that ships modernisation altogether, and been followed by Eagle as actually happened. Victorious could either have continued at Portsmouth as IRL, requiring an extra Type 984/CDS set to be produced, or her design could have been frozen in the summer of 1952 when it was first proposed to install an angled deck in her - either way the result would have been a considerably more capable RN carrier fleet in the 1960s.