Not that significant, but annoying to no end. Why does matlab has no small phi (\varphi) symbol ? It has pretty much all other symbols LaTeX offers, but not this one. Why ?
I may be wrong of course, in which case would be delighted if someone could prove me wrong…

The default interpreter is TeX actually, not LaTeX, which is why you’re having this problem. You can use LaTeX as the interpreter for a given part doing something like this:
or you can set LaTeX as your default interpretor using
which can be put in your startup.m file if you like.