OP, I think yousaythosethings might have been suggesting that the claim "transphobia is illegal" in those places isn't actually true.

I also do not disagree with your general premise, I just take issue with the phrasing. Unfortunately, overstating one's case often has the effect of undercutting it.

For the record, the other part of your title

In Pakistan, honor killings of women are legal

Is also not true.

In 2004, Pakistan finally passed a law criminalizing honor killings, and making them punishable by up to 7 years in prison and in some cases by the death penalty. But the law was weak, had a major loophole, and has not been widely enforced and prosecuted. In more recent years, it's been beefed up a bit. However, honor killings in Pakistan still are all too common, coz of longstanding cultural and religious attitudes that cause many people there to see such horrible lethal crimes as socially acceptable - even as necessary.

https://www.reuters.com/article/us-pakistan-honourkillings/pakistan-parliament-passes-legislation-against-honor-killings-idUSKCN1261OK

https://www.globalcitizen.org/en/content/honor-killings-case-study/

https://www.hrw.org/news/2019/08/22/pakistan-should-not-again-fail-honor-killing-victim

BTW, only one of your links - the first one, which is a CNN opinion piece - claims that in Pakistan prohibitions exist against thoughts, speech and attitudes that might be considered "transphobia." The authors of that piece are two sociologists who use sloppy terminology (for example, when speaking of British law, they refer to the UK as England) and don't seem to have a grasp of legal matters. They claim, falsely and misleadingly, that in passing Pakistani legislation called the Transgender Persons (Protection of Rights) Act,

Pakistan affirmed that it must respect “a person’s innermost and individual sense of self as male, female or a blend of both, or neither; that can correspond or not to the sex assigned at birth.”

Uh, no. This law gives trans-identified persons in Pakistan the right to have ID documents that reflect their "gender identity," as well as rights of inheritance, assembly, running for/holding office, and to get certain kinds of protections and services from the government.

But nowhere does this law or any other Pakistani law say that the government or the people of Pakistan now "must respect" trans people's innermost sense of themselves and their claims of having an opposite-sex "gender identity" the way the authors of the CNN piece allege.

The CNN opinion piece also notes that several years ago 50 Muslim clerics in Pakistan signed a fatwa that says

“Making noises at transgender people, making fun of them, teasing them, or thinking of them as inferior is against sharia law, because such an act amounts to objecting to one of Allah’s creations, which is not correct.”

But fatwas, decrees made by Muslim clerics, are not legally binding in Pakistan. Also, there are vast numbers of Muslim clerics in Pakistan, and lots of infighting amongst them - particularly between Shia and Sunni. Some of the hostilities amongst warring clerics are so extreme that violence and murders often occur. Just last month, a Pakistani cleric was gunned down in an assassination believed to have been done at the behest of rival clerics. So a fatwa signed by only 50 clerics in a predominantly Muslim country of 217 million doesn't really mean that much.

In fact, Reuters said that the this particular fatwa was issued by

the Tanzeem Ittehad-i-Ummat Pakistan, a little-known clerical body in the eastern city of Lahore

Lahore, BTW, has a particularly large community of men who in today's Western parlance would be considered "trans."

https://www.reuters.com/article/us-pakistan-transgender/pakistani-clerics-declare-transgender-marriages-legal-under-islamic-law-idUSKCN0ZD1IZ

Finally, if comparisons are going to be made between/amongst laws and protections for trans people versus gay people versus female people, I think it should be pointed out that most of the current laws on the books in the countries you correctly describe as "majorly homophobic and sexist" were written solely with males in mind - specifically gay and bi males, as well as straight males who are perceived as too "effeminate" for "normal" society.

In many countries such as Pakistan and India, there's been a longstanding tradition of shunting gay, bi and "effeminate" men off into a stigmatizing caste often now referred to as a "third gender." In some of these countries, persons (mostly males?) with DSDs/VSCs are also lumped in with this caste; for example, in Pakistan the supposedly "trans friendly" law passed a couple of years ago that the writers of the CNN op-ed so admire says persons with DSDs/VSCs automatically count as "transgender."

But it's pretty much the case that across the board that when laws in Islamic or Muslim majority countries have been put in place either to protect or to marginalize trans people, they've all been written by male people solely with other male people in mind. Female people usually haven't been considered at all, not even as an afterthought.