Offering a male/female protagonist option with identical strength and abilities, where appropriate to the game design (e.g. Dark Souls, not The Witcher where a defined character exists), makes a lot of sense and helps include more gamers. In those cases I suggest letting it go and playing as the male if the idea bothers you.
When a narrative-based game grounded in some degree of reality chooses a female protagonist, some level of awareness of the differences between men and women helps with immersion and suspension of disbelief, e.g. Ellie in TLOU using stealth, surprise, and blades in close quarters rather than punching it out head-on like Joel.
For an example of how not to do it, Joss Whedon has a history of casting skinny, unathletic 90 lb models as action heroines who beat up 6’2 220 lb tough guys hand-to-hand, and it’s never been anything resembling believable.
Of course, Joss was a Hero of Feminism for his Strong Female Characters, but only did it to sleep with all the starlets he cast. Game devs don’t even have that excuse.