I thought that it is the case only when you bundle into "one file"? If you don't pass the --onefile parameter, all files are in one folder without any archiving, am I wrong?
Of course you have a stand-alone executable. At least if by "stand-alone" you mean a copy you can ship to users. Which is at least the only thing I care about. And tell me which popular (say) Windows software actually comes as a single .exe. They're all many files in multiple folders. And there's no problem with that. You have one installer, which users download, which then extracts the files. Your criticism points out a non-issue.