You most likely will get full EQMs and EQPs as if you purchased full-fare F.
On your second point, the GA acted within policy guidelines. Eagle flights close the door at 10-15 minutes before scheduled departure time, and sometimes even earlier. Most GAs are very getting strict about this rule. Remember, their own a** will be in a sling if the flight is late because the GA was boarding people late and couldn't get the paperwork finalized on time.
(Don't forget that on Eagle, there are additional requirements regarding pax weight and balance that have to be computed by both the GA and FA before presentation to the Captain. Boarding additional pax changes weight and balance.)