So, right off the bat I do have found a small limitation (Granted, it is a challenging topic). I use tikz-environments, and I export the tikz-figures as side pdfs using the command
\usetikzlibrary{external}\tikzexternalize
This only works with regular pdflatex using the flag -shell-escape, as it needs to access shell tools to do that. This, shell-escaping does not work with latex.js, even when I set the flag in the latexmk_config.pl, I assume some sandboxing or something does block this. It is not a huge problem, since, if the externalization fails, the tikz-figure will be compiled in place (as is default), but pdflatex exits with an error code in such a scenario, which is a little annoying. I have no idea whether this is even fixable in the given setting.