Hello there,
I ran into the same issue while doing Nuka World first as well.
I, too, wanted to play a character that started as a badass Overboss then has a change of heart and turns good. Glad I wasn't the first one who thought of that idea.
I preped my load order with weapon mods, armor mods, quest mods and Sim Settlements 2 Suite ((SS2, SS2CH2, many SS2 addons and some City Plans)). The other mods I had that affected settlements or settlements were a couple of extra building stuff, Workshop Framework ((Obviously :D)) and Workshop Plus. I also run Complex Item Sorter with FallUI Suite.
So, after setting up my montrous load order, fired up the game, went to Sanctuary after exiting the vault, met Codsworth, took the SS2 beacon magazine, but DIDN'T go to Concord or start SS2 or meet the Stranger.
Instead, I roamed around the Commonwealth ((Playing an amnesiac Sole Survivor
)), doing vanilla and modded Quests and other stuff while avoiding settlements, and grinded to level 30+ in 4 days or so, then finally went to Nuka World.
I spent a week playing through Nuka World till I finished all the park regions ((And even Sierra's quest and the medallions)) and started "Home Sweet Home". All was well and good, till I had to place the flag in the Settlement. The 3 flags at the Raider Category>>Flags were dimmed. Didn't matter which settlement I picked from Shank ((I tried Nordhagen Beach and Greentop Nursery, both never been visited before)) or which gang I choose, the flags stayed dimmed.
I was sooo frustrated and I didn't want to start turning off plugins to find the culprit, so I searched online for an answer and found this thread. I never expected SS2 to be the culprit, but I did a test. I went to a save before I talked to Shank, I disabled ALL SS2 mods ((Along with any other dependant plugins)) and played through "Home Sweet Home" without issues till it was finished and "Power Play" started. I even played through power play just to make sure everything went smoothly.
Funny thing is, I am surprised the game loaded even after the many mods I disabled to do this test XD and didn't CTD once.
THE DEFENITIVE CONCLUSION: Sim Settlements 2 halts Nuka World's "Home Sweet Home" quest.
SOLUTION:
1) Either play Nuka World and finish it first BEFORE installing SS2.
OR
2) Install SS2 and play Nuka World normally, and when the time comes to place the flags when claiming the settlements, use the tgm console command to place them.
Sorry for ranting XD.