Both my mother and my father have worked in the software industry (though before version control was the norm). I don't find either version offensive and I don't see any problem with a silly quip implying my father uses a version control system unlike the one being described.
EDIT: It occurred to me that my story goes even deeper.
The syntactic template "Not your father's X" is a reference to a well known ad campaign by General Motors. "Not your father's Oldsmobile" the slogan went. It was clearly an attempt to remove the strong association with an older generation that the brand had among younger buyers. It couldn't have helped that the nickname for the brand was "Olds", but that association was also somewhat based in fact: the car was indisputably a favorite among old people. Once at a family reunion I noticed that most of my aunts and uncles drove Oldsmobiles, with a few Buicks thrown in for good measure.
Note that another effect of this campaign also worked to discourage the perception of Oldsmobiles as appropriate for specifically male buyers. Clearly they wanted all the buyers they could get. So "Not your father's X" seems constructed to actively remove gender stereotyping, not reinforce it.
Apparently the ad campaign didn't work well enough, as GM stopped producing new cars under the Oldsmobile brand a few years ago.
Indeed my father did have an Oldsmobile for a few years, during which he had a software startup. However, he had inherited it from my grandmother when she died. When the AC broke in a way that was not economical to repair my dad went back to driving Toyotas and he gave me the Olds. So that actually was my father's Oldsmobile (but I associated it more with my grandmother).
That reminds me, I've been meaning to ask Dad what kind of source code control system he's using these days...
The alternative isn't "Not your mother's version control" but rather "Not your parents' version control". Neutral should be the norm. Not a big deal, but there is a lot of subtle sexism in tech and it adds up at the end of the day.
My parents divorced before version control was commonplace, how dare you imply such a thing!
Assuming that because "his" is listed before "her" there is a gender bias is taking things way too far - since language is a linear medium, you have to pick one to be in front, and I think most people understand that it's not trying to give the choices an inherent order.
"his/her" is a bit of a bugbear of mine in any case, not only for the ordering, but because it lacks cosmetic elegance. "They" is an ideal alternative.
It is interesting to note that in most figures of speech, the male variant is listed first. For example, "his and hers", "Mr and Mrs", "he and she", "his/her", "Lords and Ladies". Yet, "ladies and gentleman" is a popular counterexample. Funny stuff this English language! ;-)