I cannot get the Mechanist to stand down. Everything I tried and she becomes hostile as soon as she comes down. I even tried taking the elevator after getting all 3 holotapes and she still became hostile without talking.

Take off your PA helmet. I had the same problem.

I searched and found the culprit. It cane be one of two known things. It seems the targeting HUD you can install on Power Armor can do it and if you are using a weapon with AoE during the last battle you can injure the Mechanist or Sparky through the wall making them auto hostile as well.

Another bug I encountered was CTD after completing the last quest when I tried to leave the lair via a door or when I traveled too close to the lair. Some mods that change the UI can trigger this, the culprit are some mods that add or change .swf files. No dotdotdot is a known culprit. It seems when you get close enough to the mechanist lair for the map icon to appear on your compass it will cause a CTD with some .swf file changes.

There is simple mod on Nexus that changes that one specific icon to a Vault icon and that seems to be working if you do not want to remove the mod(s) causing the problem.