Schaeffer’s comments about the character explain quite a bit. What fans saw as a reference to some major appearance was actually a heartfelt tribute to a dear friend, with the prominence given to the character actually reflecting the personal importance of the name.
Speaking with The Daily Princetonian, the student paper of Princeton (Schaeffer’s alma mater), the showrunner talked about the real-life origins of the aerospace engineer, revealing that the character was actually a reference to one friend out of a group of “extraordinary women who live all over the country, who do all kinds of things”:
“You know, the character that Monica [Rambeau] met on the show that everybody thought was going to be Reed Richards, the engineer? That character is Major Goodner, and she’s named after one of my friends, Aly Goodner [’00], that I went to Princeton with, who’s part of this group. I made that choice because that character represents every time one of these women has come through for me and every time they’ve been good at their job.”
Considering the show’s massive amount of references to the MCU and the wider world of comics, it makes sense that fans started to look for little teases like this everywhere. Even so, many ultimately only distracted from the core of the show.