So my current character is not doing things as directed by the game.

She skipped Concord and triggered the MQ by doing the Memory Den in Goodneighbor. That lead her to Nick Valentine, Piper and a very cool intro for Dogmeat. This also gave her an alternate introduction to the Brotherhood of Steel who showed up in the airship after she killed Kellogg. I got a quest to investigate the airship and was directed by one of Ashley William's many clones to go find Danse at the police station and that he was in charge of recruitment.

But I am getting off track here.

Eventually since I try not to fast travel, my character on her way back to her fortress of solitude in Sanctuary Hills happened upon Concord. There she slaughtered the Raiders and helped defend the group trapped inside the Museum of Freedom. But after killing the remaining raiders and deathclaw (with the help of a random encounter of BoS and a Vertibird) She didn't bother checking in with them. In her mind they figured out it was safe to leave and go where they wanted. Plus I am not eager to have them invading her fortress of solitude.

However I wonder if I might have botched things up should I start the Minutemen quest. Either if forced to by the MQ or if I want something to do. You see I just came across the Castle while visiting the nearby Atom Cats. And because it is something she would do, I cleared it, fortified it, powered it and put up a settlement beacon. But now I wonder if this will botch up the MM quest to take back the castle. I already cleared it out, destroyed the nests and even killed the mirelurk queen.

Has anyone else done this before being asked to by the minutemen? Or if since I have no interest in joining the MM, this quest will likely never come up?

The castle is only important to the Minutemen, so you could do whatever you want if you never deal with them.