You miss a lot by avoiding the MM questline. The secret lies in developing settlements you actually want to have and connect them with supply lines. You don't have to develop each one of them.

Settlements are actually only activated by using the red workbench in them, if you don't use that, you don't activate the settlement.

Clearing them doesn't automatically open up the settlement.

Thats not true, I haven't used the workbenches but have 7-8 settlements I can send companions too which means they are my bases

But you don't have to use them. If you don't build anything at all there, don't send any people there, they will never bother you again.

Did you do quests given to you by people at those settlements? That's the only other trigger.

no I avoided MM but I do clear, read, pick up everything in those areas, maybe that is the reason.

Not all the quests given by people at these places are obviously MM quests. Finch farm as an example.

But as pointed out, unless you actually build something at those places, ie: build a recruitment beacon, you don't have to take any notice of the settlements.

the MM settlement quests have mostly been random for me after 2 playthroughs now, so at least you'll have that going for you...you may know most of the settlements, but you wont necessarily know where you are going to get sent...