This is an unnecessarily alarmist post.
As described here, you absolutely can create Perspective's extra resources (fonts, themes, icons) now by directly editing files on disk. The location is different and two extra files are necessary - that's the only change. For themes, take the same instructions I gave for icons, but in your config.json have a single entry "entrypoint": "someFile.css" that points to the 'primary' file. For fonts, create an empty JSON object in the config.json.
The overall structure of the theme/icon/etc files has not changed - you can extract them from the module easily with an archive explorer if you want to open them in an external code editor.
As mentioned by others, that restoring an 8.1 gateway backup doesn't properly restore all theme resources is a known issue that we're going to fix.