Org is really just a text format, like Markdown, and the core format hasn't changed in ages. So I don't think there's a sync problem here with respect to the applications themselves.
The more likely pain-point is that on one device you have extra tools/configuration set up (e.g., org-latex), but these tools aren't available elsewhere (such as in orgzly). But I assume that this is a given for orgzly users: they probably don't expect they can do everything that org-mode enables in Emacs (like producing PDFs via LaTeX). They just want to do basic edits, and don't want to lose data when the document round-trips between Emacs and orgzly. (I don't use orgzly, but I assume that safe round-tripping is a feature...)
The more likely pain-point is that on one device you have extra tools/configuration set up (e.g., org-latex), but these tools aren't available elsewhere (such as in orgzly). But I assume that this is a given for orgzly users: they probably don't expect they can do everything that org-mode enables in Emacs (like producing PDFs via LaTeX). They just want to do basic edits, and don't want to lose data when the document round-trips between Emacs and orgzly. (I don't use orgzly, but I assume that safe round-tripping is a feature...)