Now one has to be fair when making this kind of statements.
First of all: how 'big' is this incompatibility? I think that it is not that big at all and roughly as big as when you use a new style package with LaTeX or when trying to recompile a 25 year old LaTeX file.
Secondly: who is to blame for this incompatibility? TeX/LaTeX was designed to have a Turing complete grammar, which makes it impossible to write 100% reliable converters. The way the comment is stated, it suggests that TeXmacs is not good enough. I think that this is a misrepresentation.
Now it is plausable that the author is not even aware of the implicit bias of the terms 'incompatible with LaTeX' and 'partial converter'. Therefore, my reply might sound aggressive. But if you carefully reread it, then you will understand that it isn't.