OK what do we actually do about gender?

Well, let's look at a couple contradictions.

The manifesto speaks of gender's material base being in the sexed division of reproductive labor. This has been falling apart steadily since the 19th century. Proletarianization and mechanization degenders labor, and the time needed for homemaking has greatly reduced due to industrialization. The two things that remain are birth & childcare. However, birth rates across the developed world are below replacement rate, so it would be accurate to say that patriarchy & capitalism have become a fetter on the continued development of humanity. However, the reproductive technologies necessary for feminism & communism are underdeveloped. Although sex is no longer necessary for reproduction, semen still is, and biology is gendered under patriarchy, so this is a potential issue. Additionally, uterus transplant technology is in its infancy, and people still need to bear children themselves. Of course, these limitations would be less important if humans didn't still die of old age. So, if you're a biologist, you can do your part in abolishing the regime of gender by advancing reproductive technology or curing aging somehow.

The manifesto provides five characteristics of the modern patriarchal system. Number two is:

These two genders are seen as identical to your biology and fixed from birth. While every gender system ties gender to biology, the modern system equates the two. Being a man in this system isn’t tied to having a penis, it is having a penis. And this gender is immutable. You can’t change it. If you’re born as a man, you’re seen as a man no matter what. There are no options or alternatives.

Actually, the Gender Accelerationist Manifesto is a bit lacking in commentary on this aspect compared to Gender Acceleration: A Blackpaper. The issue with this conception of gender/sex that many gender accelerationists raise is that it's 1) obsolete 2) increasingly unviable. Really, HRT allows one to change their sex, because no one actually has Superman's X-ray vision. Industrial society has had the means to completely tear apart this biological conception of gender for nearly a century at this point. Simply mandate puberty choice and have teens pick the hormones they want. Of course, patriarchal society is incapable of doing this, but eventually it may be forced to. The Blackpaper states,

Recent studies, most famously one in 2007 and one meta-analysis of 185 studies from a total of almost 43,000 men referenced in a recent GQ article, show two things. There is without a doubt a staggering decline in testosterone, so much so that within a generation humans may become completely infertile.

Human reproduction is becoming a quaint, unnecessary and ultimately purely elective act, and further evidence suggests that sperm is rapidly decreasing not only in quantity but also in quality, positioning the drive towards reproduction, the utility of reproduction, and the ability to reproduce all on a slope of ruthless decline.

There is also the fact that there's a secular decline in the age of puberty. In Denmark, it begins before the age of ten. Maybe people will finally start to be alarmed when the majority of girls are growing breasts at eight?

If patriarchy and capitalism are still around in a couple decades, not only will sex be forcibly assigned at birth, it will have to be forcibly assigned again years later through exogenous sex hormones. Everyone will be on blockers, and the half of a child that each couple will be having will be conceived through reproductive technologies. At this point the whole biological justification will become a clear farce. Advocacy for universal puberty choice would probably become a serious issue rather than a fringe one held by a few hundred communists.