In the case of the Bogue, you're correct in stating there were 4" guns. But the vast, vast majority of its weapons were 40mm Bofors AA guns and also 20mm guns, guns which are unsuitable for being in an R or T battery. Unless there is am implementation for these to shoot like slow-firing pom-poms at enemy ships I don't think it's necessary to make these an R or T battery.
The Independance carried purely the 40mm Bofors guns. No heavy weaponry here.
With the Ryujo - the current implementation is enough. All it had in the way if guns was the 6 R slots that are in it today, 127mm DP guns. The guns you circled in black are 13.2mm Hotchkiss machine guns.
With the Essex, I don't think you correctly evaluated the armament. The four mounts that carried 5" guns (implemented in the game) were only half of the carrier's real armament. It also carried four 5" singles at the bow and stern like the Yorktowns. The mounts you circled in black in this one were, again, 40mm Bofors and 20mm Oerlikons.
I agree in the statement that Enterprise is accurate. And I also agree that the Lexington's 5" battery should be included. We're talking twelve 5" singles here and I wouldn't call that easy to ignore.
There could be a reason behind all this, to put the carriers in their proper tiers and such. Though this doesn't seem to be all across the board. Essex, with only 4 R slots to Ticonderoga's 8 (here they employ the port side slots that housed 5" singles, bow and stern), is relatively balanced to it, although both carriers should have exactly 12 mounts, including the 5" single mounts on the starboard side. I suppose that excuse could be used.
And you shouldn't exactly cover a blitz-level carrier with anti-ship weaponry, either. That could cause the less-intelligent players (we all know they exist) to do dumb things in Blitz, for example. Carriers with strong R batteries exist in Blitz because there is already a check to this - the battleships will always have far greater gunpower than a CV. Besides, the CV's are not meant to be gunships and many CV's will just neglect their gun slots.
Lexington, though, is a CV5. The 5" singles there should be implemented. As for the gun slots, inadequacies in crew leveling exist all across the board in multiple shiplines and nations. Take the IJN Tsukekei destroyer. If you want to level a hybrid crew, for example. The Tsukekei has no torp slots, so you either put your torpmen on the support slots or take them off, and you know you're not leveling them. Does Tsukekei get 5 support slots instead of 3? No.
So moral of the story - you just need to find a way around it. PS - Dixmude is considered by most to be a CV2, not a CV1...