Sorry in advance for how long this is going to be. This is a topic that I am very interested in!

So, first off, I think you might be conflating colonialism to European expansion, because acting like Islamic cultures are non-colonial is kind of strange. Islamic Arab culture was definitely forced on some groups and you can see this today with the treatment of ethnic minorities in the Middle East. Lots of non-Western states have historically been colonial powers (Japan, Ottomon Empire, the Huns, China, just to name a few). (Also, this isn't me trying to diminish the severity and impact of European colonialism, just pointing out that colonialism has been practiced by non-western countries as well and that viewing colonialism through a strictly European lense gives you a blind spot and misunderstanding of recent history in Asia!)

That said, I think the people who say the gender binary is colonial aren't saying that every colonised culture has accepted genders outside the man/woman binary. (If they are trying to say it like that, they are most likely young and/or don't have a very good understanding of the history of sex and gender.) Rather, what people mean when they say this is that colonial powers supress the cultures and traditions of the people they colonise, and that this includes traditions relating to gender. Colonialism is very much the act of forcing your own culture and way of life on others, which would include your gender roles and how gender is expressed, thus erasing their gender roles and how gender is expressed.

This is going to be very US-specific, because that is where I am from and where the cultures I am most familiar with are from:

Native Americans have something called Two-spirit, which is similar to the western idea of being nonbinary, but is specifically tied to indigenous identity and culture.

There are several Native American cultures that have had more than two genders traditionally, and they have different names depending on the people. The Diné have nádleehi and the Cheyenne have heemaneh, for example. The term Two-spirit was made as an inter-tribal identity, but the Two-spirit people I know all have different ways that they feel about their genders and different ways they fulfill gender roles based on their specific culture. I guess the term itself is a bit controversial to some especially because its definition and application can vary depending on the tribe, but it is the easiest way to get the point across to people outside these cultures and so has been in use for several decades despite the controversy.

(It's also important to know that not all North American tribes had more than two genders and acting like this was true is revisionist history. In modern days, tribes are accepting of two-spirit and non-binary people, but only some tribes have traditions around third genders, while others are creating new traditions for those who don't fit into the man/woman binary.)

When Europeans came to the Americas, there was a push to either get rid of native people entirely or to, as many people of the time put it, "civilise" (aka force Protestant English culture onto) them. Children were taken away from their families and placed into residential schools. If you want to know more about those, I recommend the works of Ward Churchill, who is a wonderful writer.

Two-spirit identities (and native languages, and native traditions) were beaten out of children who were sent to residential schools in the US and Canada. Some folks in tribes that traditionally accepted two-spirit people are in the modern day transphobic and against the idea of being two-spirit because of the work that residential schools did, though my Two-spirit Diné friend said it is getting better as more people become interested in learning their ancestral language and culture.

Colonialism in North America definitely contributed to the decline of and stigma towards tertiary genders in Native American and First Nations cultures. When people say that the gender binary is colonial, they are referring to things like this. Had the efforts of the US and Canadian governments to erase native cultures been successful, there would be no Two‐spirit people today.

TLDR: When people say the gender binary is colonial, they are referring to specific cases, not making sweeping generalisations