While I agree that they should be added at some point, these are different cases.
There was no intention to arm the EAP or Su-47, the YF-23 would only have received weapons for testing, had it won the competition and the F-15MTD was a research aircraft.
The MiG 1.44 is a bit of a weird case as they may have intended to integrate weapons for testing, but as far as I know, they never got around to doing that before the project was cancelled in favour of the PAK FA project (Su-57).
The EAP was always meant to demonstrate tech that would go on to be used in the EF Typhoon, the Su-47 was mostly experimental and there was no intention to adopt that design and the F-15MTD (later F-15 ACTIVE) was used as a research vehicle to help with the development of technologies used in the AFT programme (F-22).
The YF-23 could qualify for a Yak 141 treatment.
Equip it based on a “what if we ended up with the F-23 instead of the F-22” scenario.
The MiG 1.44 could be treated similarly.
Meanwhile the planes in the game that lacked guns IRL really just did lack guns and nothing else, they were ready for adoption and just needed to get the go-ahead for production.
Still has nothing to do with being a “4+” gen even if it was added with its non existent armaments. Pretty sure there is no evidence it was ever even ment to have anything else