In order to take the settlement, everyone must be killed, except Dora and Deezer. If the Sole Survivor decides to side with Covenant and completes the quest with dialogue options, then the town will allow the Sole Survivor to join without any conflict. Speak to Jacob Orden to obtain access to the workshop.
Inside Covenant, players can find a few things that raise suspicions, like an abandoned bed roll, a note that talks about the rules of Covenant and how not to talk about Synths, and self-help books. Yet, none of this leads to concrete evidence of the fate of the caravan's survivors, or Covenant's involvement.
If you are not worried about role-playing just let Amelia die. There are no repercussions for doing this and it keeps the settlement friendly.
Inside Covenant, players can find a few things that raise suspicions, like an abandoned bed roll, a note that talks about the rules of Covenant and how not to talk about Synths, and self-help books.
If you destroy the institute, the covenant quest chain no longer starts. You need to acquire the settlement earlier in the game.
Visitors to Covenant are subjected to a psychological test, called the SAFE test.
You pass no matter what because all the choices are 'human' answers. I get that it's a throwback to the GOAT, but I wish they would have thrown in a speech check that would lead him to believe that you are a synth.
Inspecting Amelia's body after death reveals a synth component on her corpse, meaning that she was indeed a synth.
If the original inhabitants of Covenant have been killed, any remaining turrets in Covenant will be hostile towards new turrets, the player character and hostiles.