I concur. Really great post! Been an engineer for a while, starting to prepare to put together SaaS products, so this will be useful to come back to. Thank you, OP!
I write a lot of LaTeX documents and use the TeX Live distribution to typeset them, so I understand why the name TeXMe could cause some confusion.
This project only cares about protecting the LaTeX content (the MathJax supported LaTeX, not the "real" LaTeX) by hiding it from the Markdown processor, so that the Markdown processor cannot mangle the LaTeX code before it is fed to MathJax.
I could have named it MathMe, JaxMe, or something similar that would have eliminated this confusion between MathJax supported TeX/LaTeX[1] and the "real" TeX/LaTeX. However, unfortunately I did not spend sufficient time thinking about a good name for this project, thus the name TeXMe.