I'm wondering if this would have any impact on performance at all, if done right.
document.getElementById('flarum-loading').style.display = 'block';
is run directly on the page so it runs at the very first possible moment, I don't think it would be wise to move it to a file.
However the javascript code at the bottom of the page is only run after the two compiled scripts (app and language) are loaded, so it's clearly not put there to run at the same time the source page loads. I think it's made that way because it needs to wait for these two files to load, and loading a third file just for that would probably have a bad performance impact. as pointed out by Pollux
But if the code was changed so both app and language are in the same external file, then all this bootstrapping code could be embedded in that file as well.
Maybe a first step could be to move everything except app.boot
inside one of the external files. It's really only the boot that needs all the other dependencies loaded before running.