I want to also add that this extends to the birds themselves, their eggs, AND their nests.
As far as I know, Indigenous folks also do have to apply for a permit still on an individual level. A random person can't roll up, claim to be from whatever tribe (even if it's true), and keep feathers and stuff from the birds protected by the treaty with no proof or permits.
This is also true of exceptions made for breeding, hunting/depopulation, falconry, and scientific/educational purposes! Educational facilities can apply for permits to keep parts or whole animals (alive and taxidermy). While I was in grade school, my mom found a great horned owl on the side of the road that had clearly been a victim of car-strike. She was able to call around and get permission to take it to a taxidermist, to be mounted for my elementary school. That owl is still on display there! My college had a taxidermy class, and I've transported several window- or car-strike birds I've found to them to be used for classes/archiving the pelts.
Falconry is, at least in my state, a 2+ year apprenticeship before they are allowed to have their first bird. They can keep a certain number of certain kinds of feathers for the purposes of imping (wing/tail repair), but are not allowed to keep "keepsake" feathers once the bird is no longer in their care. It's really strict and kind of hard to get into.
And for falconry, some of the birds are bred, and some are wild caught. So there are exceptions there for breeding for this, and presumably for zoos and other conservation/education facilities that do breeding.
Some species, like the Canada goose and some other water fowl, ARE protected, BUT also have a hunting season and regulated take. This requires a hunting license to do. Taxidermists who work on legally taken MBTA-protected species I believe also have to have a permit to do so. Some places, like airports, have permits to clear hazardous birds from the runways/airways; most places are not allowed to mess with, for example, a nesting Canada goose. Shutting down air traffic for a month over a Canada goose nest would be extremely disruptive to many many many people. Getting a Canada goose or several Canada geese sucked into a jet engine is probably not ideal. So, they have permits to chase off or even sometimes depopulate birds causing issues at the airport.
If you're interested (or worried), you can read the MBTA here!