Not all of them, some you just need to clear to claim.
I use this map for many F4 things: http://www.fallout4map.com/
The answer is NO , you do not need to be allied with MM .. The settlers will give you things to do and when done will give you access to the workshop .
You just need to goto each settlement regularly .. and Yes , you can also have supply lines
^ This. Plus others you can get just by clearing the area and opening the workbench.
To be honest I've got some both ways, I secured several before joining the MM and later I joined the MM. Can't really tell the difference but I do believe the MM count them as theirs as I could immediately do some other MM quests that generally require you to have a specific number of settlements already.
But really no difference anyway. It's not like they are flying a MM flag or anything. I did help one that wanted some Gunners killed last night and when thanking me they mentioned the MM were the one's helping them, and this was a settlement I got before joining the MM. So I guess it's assumed they are all under MM control now. But again, it really doesn't make a difference in how you treat them. Preston isn't going to ask you to help a settlement to get them to join if you already have that settlement but he may ask you to help them, but the 'now join the MM' options won't be there.
Beyond the ability to build artillery through the MM story line and some Minutemen settlers at the Castle there is no difference between MM settlement and a non MM settlement.
The existing settlements still give you the radiant quests even if the MM don't exist and If your in the MM the game assumes all of your settlements are MM settlements.
No. In fact I seldom see them even now and I've got 15+ settlements running. Granted I've never used the Flare Gun to summon any, but then I've never needed help in a fight either. In the time it takes me to switch to the Flare Gun and fire it in the air I can kill whatever is bothering me. I may have to do it once though just for kicks. With all the settlements I have I should get a lot of backup ... and maybe more bodies to loot afterwards.
I don't ever remember seeing minutemen at any settlements. At some point they seem to take up positions at "checkpoints." and you'll sometimes get 'help defend the checkpoint' missions when running around. Those don't seem to be anywhere near settlements though. .. I also can't figure out the importance of those checkpoint locations. I originally thought they were along settlement trade routes.. but there are some just out in the middle of nowhere, so.. who knows.
I saw one MM patrol in 90+ hours of gameplay with every settlement built up.
They like the other factions set up checkpoints after their victory, but that was about it for me.
If your not using the flare gun or artillery they are pretty much non-existent as a faction in the world.
The checkpoints seem to mostly at or near a Power Armor locations, handy if you haven't already located them.
Oh I love artillery! I've got to the point now where I put all spare settlers on artillery cannons. When I call in the shots the sky lights up. Great for clearing out Raider and Super Mutant strongholds.
Ahh, good eye. I guess I slightly noticed that but since I had already collected all the power armor I didn't put it together.