A lot of boomer shooters nowadays have a female protagonist, e.g. Selaco[0], Supplice[1], The Citadel[2] and its sequel[3], Zortch[4] (and its upcoming sequel[5]), Nighmare Reaper[6], COVEN[7], Viscerafest[8], Hedon[9], etc. If anything i'd say that nowadays there are way more boomer shooters with female protagonists than not :-P (combining the tags "boomer shooter" with "female protagonist" on Steam search gives 143 results, though that includes games where you can either choose your character's gender or you play as a woman for a part of the game even if you play as a man for most of it).

[0] https://store.steampowered.com/app/1592280/Selaco/

[1] https://store.steampowered.com/app/1693280/Supplice/

[2] https://store.steampowered.com/app/1378290/The_Citadel/

[3] https://store.steampowered.com/app/3371240/Beyond_Citadel/

[4] https://store.steampowered.com/app/2443360/Zortch/

[5] https://store.steampowered.com/app/3807500/Zortch_2/

[6] https://store.steampowered.com/app/1051690/Nightmare_Reaper/

[7] https://store.steampowered.com/app/1785940/COVEN/

[8] https://store.steampowered.com/app/1406780/Viscerafest/

[9] https://store.steampowered.com/app/1072150/Hedon_Bloodrite/

"boomer shooter": 1105 matches

"boomer shooter" + "female protagonist": 106 matches.

So a bit less than 1/10 of the games tagged with "boomer shooter". With your caveats above about being able to choose a gender, or a single brief segment where you're a lady in a game where you're mostly a dude. Is that a lot? I dunno, doesn't feel like a lot to me. Probably feels like a lot to the people who inevitably show up in the Steam discussions of any successful game that makes you be a lady for most of its length and complain about it being "woke", even one game with a female protagonist seems to be too many for them.

143 results means it's relatively rare.