The same sizes show up using pure Latex.
Gives (compiled with pdflatex)
And this is inside Mathematica:
I do not see any difference. But I think your question is really about Latex itself and not Matex, which just compiles using Latex.
You could see this how-do-i-create-an-invisible-character on Tex Exchange where it says
\phantom inserts an empty box with the same dimensions (horizontal as
well as vertical) as the argument
But if you think it is not doing what it should, I would suggest asking at https://tex.stackexchange.com
What you want is
\hphantom and not