I've just run into this issue myself. I hadn't played a Raider in a while and felt like giving it another go. I haven't tested any of the aforementioned workarounds yet. I believe SS2 was recently updated, though I'm unclear on if that update contained a fix for this as I haven't gotten the update yet. The really unfortunate thing was that I wanted to play it like my character was starting to become the benevolent leader of the Commonwealth, then hit a really rough patch and hit a spiral that set them on the path to becoming a raider. Which meant playing with SS2 early on. Theeen this. Ah well. I'll try some of the above workarounds and report back if any of them get me through Home Sweet Home.
EDIT: I can confirm that the solution mentioned above by TechTonic does work. However, it's the only way to get it to work naturally without the console, cheat terminal, or additional mod to just bypass this feature of Nuka-World entirely. You have to take the peaceful/charisma option and it has to be a settlement you already hold. The problem also persists beyond Sinner and likely throughout the entire rest of the DLC. Just as a test, I tried choosing violence on an owned settlement and, when I got it, I was unable to place a flag. This was after I'd already used the above solution to get my first outpost and scare Sinner off. You have to choose this option every time, I've observed. Go to an owned settlement (or force a settlement to become owned through management), then go have Shank set up the job and pick the peaceful option. I'm as of yet uncertain about vassals. I'll update again when I've tested further.
EDIT 2: Vassals are also broken, though I can't say, for certain, if it's because of SS2 or something else. Shank did let me go beat up or talk to pre-existing settlements to convert them into vassals, with the distinct exceptions of those that had quests attached to them - them being Tenpines Bluff and Finch Farm (probably others too, but I haven't really tried beyond those two). You can still go kill everyone there to claim an outpost though. I accomplished that much with Tenpines Bluff. You can't select either of them if you haven't completed their quests. However, if you do complete their quests, they're still broken. You can't actually take them as vassals. If you try the peaceful route, the objective to talk to the NPC won't actually be assigned, just the optional objective to set up the Nuka-World Radio. So you can't talk to them to set up the vassal. If you choose violence, you don't get the mission at all. (Note: Abernathy Farm and Tenpines Bluff might be workable if never actually do, or even get their quests. I assume Finch Farm is a lost cause because of the nature of the Ironworks quest. Same with Covenant) You also cannot establish vassals using settlements that were previously empty and that you've built up. I tried setting up Sunshine Tiding Co-Op and the Egret Tours Marina as settlements so I could later come back and have the Nuka-World Raider bully them for supplies. Didn't work. Another thing related to the inability to use violence to establish an outpost is that if you do use the cheat console to fix it, the game doesn't seem to actually fully acknowledge the settlement as a new Raider outpost. I dunno if this affects anything, but the icon on the map doesn't actually change from the base one to the Raider one in these scenarios.
Addendum: This doesn't really have to impact your game, technically, but it does basically mean there are certain settlements that you can't take over as outposts if you want as many vassals as possible. Notably, this playthrough has made vassals of Greentop Nursery, the Slog, and Nordhagen Beach. I'm not sure, but you might be able to get Abernathy Farm, Oberland Station, and Tenpines Bluff as vassals too, but the latter may only be possible if you never pick up Preston and company in Concord. You could probably also get County Crossing as a vassal as well. Everywhere that's empty or held by a hostile faction is free game for an outpost, which is more than enough to get the 8 outposts for the Wasteland Warlord perk, though you wouldn't really need it since you're going to be using the Cheat Terminal to set up outposts in the first place (otherwise you wouldn't be able to place the flags). Finch Farm and Covenant are the only prepopulated ones I can think of that'd have to be made into outposts.