Yes, they did. Arduboy Community also did.
And I mean it make a lot of sense, because these chips are not awfully expensive. The ATmega32U4, for example, is $4.6 among this chip shortage madness. Yes, a ARM m core is way more cheaper, but that's in part because the 32U4 is old.
Like how Arduino used 16U2 for their programmers of Due, Mega and Zero and such. Because they need a microcontroller with these capabilities (e.g. native USB handling), they just grab whatever that is off the shelf.
It does not matter whether its open source or closed source. Earlier on you had Atmel Studio. Now that Atmel is dead, Microchip took over and you have Microchip Studio for their(or anyone's) AVR and SAM devices
How nice.