It depend on what you mean by safe. As mentioned by @dbuenzli, with the next version of jsoo, jsoo link will perform some compilation unit pruning for libraries. So cat will not longer be equivalent.
jsoo link also does the merge of sourcemap when requested.
jsoo link is supposed to be fast (but maybe when sourcemap is requested). In particular, it doesn’t parse the javascript. I don’t know what you’re trying to achieve, but if jsoo link is too slow for you, contributing to jsoo could be a better use of your time (compare to working around the tool).
I’m curious, have you witnessed jsoo link being slower that esbuild ? do you have numbers ?