Do the Mechanist' robots act as they usually do? Namely shoot anything on sight, if she is around them or not?
The ones with her are on 'bodyguard' mode, and so will only engage targets who attempt to harm the Mechanist directly.
Other robots she's built are on 'combat patrol' mode and seek out and destroy anyone they consider to be hostile, which given the faulty logic of the Robobrain supervisors is anyone who isn't the Mechanist.
Given that she has to work her way through central Boston to get to Scollay Square, right through the middle of the Supermutant settlements, it's likely to take a couple of days in-game before Isabel arrives in Goodneighbour. She's not going to be too subtle about her approach though, so any faction monitoring the area will likely find out about her movements.