No, I don't think reading transgendered story books to preschoolers is anymore indoctrinating than reading non-trangender stories. Books make people think, not the opposite.
Homosexuality is entirely different from trangenderism. As is often spoken in defense of public bathrooms, people around here seem to think transwomen will rape women. Which appears to at least justify that perception that transgenderism isn’t as explicitly tied to homosexuality, does it not? And in my experience with speaking to such both transwomen (and the often overlooked transmen) appear to prefer the sexual company of women no matter how they identify. Trans or otherwise. While that may be homosexual in nature, it is not exclusive to the possibility of a biological heterosexual couple despite transgenderism. Though even that can be extremely rare.
In short, it’s complicated.
The purposes of the books is not to turn children homosexual or trangender but teach tolerance of different people. If that is the sort of “indoctrination” you are against, then what are you trying to indoctrinate to these children? Your own perceptions of people that you do not know or speak to?