Post script to my prior post - I made the transfer this week between American and Cape Air in both directions at Logan.

On the outbound leg, my American flight was about 40 minutes late in arriving. Running as fast as I could, I was able to go gate to gate to Cape Air in about 10 - 12 minutes ( including sprinting through the parking lot and then down the long hallway to the other terminal, checking in at the Cape Air counter, going through security again). I made it just as my flight boarded.

In the other direction, Cape Air was indeed able to print my American boarding pass. However, it did not have TSA pre-check printed on it, so I stopped by the American counter and had them re-print the boarding pass with pre-check indicated.
I was not able to retrieve my American boarding pass electronically through the AA website, as it indicated I needed to check in with Cape Air instead.