Sorry to jump on this thread but I might be either 1) having the same issue or 2) being way too impatient.
I started a new game with Conqueror, waited in the vault until Stage 4 had completed, left and Sanctuary and Red Rocket were unchanged. My previous playthrough was using SS and Leaders to auto build and upgrade settlements etc and never had an issue, so presume my regular mods shouldn't conflict with Conqueror. However, to play it safe, I've started another new game with the only mods being UF4P, AWKCR, SS 3-in-1, Workshop Framework, Conqueror, all City Plan Contests (are they all needed??), HUDFramework and SKK Fast Start. This time I'm currently standing outside the vault watching over Sanctuary. Halfway through Stage 1 and not yet seeing any changes.
How soon are changes 'visible'? I might have been too quick to assume changes would occur as with regular SS i.e. new plots visible, foundations/walls being laid etc. Will changes only be visible after Stage 4 is complete AND a specific in-game time passed? I'm not sure I want to be waiting 3/4 hours for the process to complete each time to see if it's worked or not. I mean, settlements being pre-built before leaving the vault is a big attraction for me. How will I know it's working?
PS: I was looking to follow the Raider play-through so didn't go to Concord to find the mission start. I was actually hoping for settlements to be fully built, then fire up Fallout 4-76.