Yes the flag on the mod stays false as you can see in the screenshot (this is one of the last renders of the last update, so it has all the content available) and the KayleeSex4 flag still is false but it didn't made me lose any content with Kaylee, you can see there KayleeSex5 as true. I guess it is just a visual glitch and the KayleeSex4 simply didn't went true as should. But doesn't bother the gameplay. So no need to worry about it
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If you didn't pointed out I wouldn't ever notice it hehe I usually notice this variables only when I don't get some content for any reason lol
When Sancho gets back or when game has a new version probably Sancho adresses this glitch, isn't a critical one so no rush. Well I hope Sancho gets back, I love their mods, but I never notice so many days without news from Sancho. But even in the worst case and Sancho doesn't come back, there is always the file to fix the modded saves to work unmodded.
Edit: I just checked the MrBubu pdf walkthrough and every time in season 2 is checked Kaylee path content the only variables into account to enable more content with her is from KayleeSex2 and KayleeSex3 variables. Never is the KayleeSex4 so I would guess it is a "sterile" variable that is used for nothing going forward, maybe that was why Sancho kept it false lol just as a "joke" because it is a for nothing variable hehe, Sancho teased a bit Classy Lemon (the dev) about some of the code gets useless and that the code could get some cleaning while doing the mod hehe but was all in good fun.
I could use the universal mod URM to check variables but usually I avoid URM, it annoys me and it is very intrusive imho. Some people only use that in every game, I still prefer author mods for each specific game and being the least intrusive about all the variables and labels in the game. I like info and guidance (with the least spoiling possible of course) in my games but don't care about code specifics