Maybe it's just me, but why can't Matlab just use the Latex fonts in an EPS, and output that EPS as a single file? That sounds like a more robust and less convoluted solution.
But everything in MATLAB, then I just symlink the pdf figures to the manuscript folder, so with an F5 in MATLAB and a build in Sublime I have the manuscript updated.
You could probably do the same thing but do the export of the tikz file instead of the PDF. That's basically what I do.