Bookmarklets and the JS console seem to be the workaround.
For very large customizations, you may run into browser limits on the effective length of the bookmarklet URI. For a subset of well-formed programs, there is a way to store program parts in multiple bookmarklets, possibly loaded with the assistance of a separate bookmarklet "bootloader", although this would be tedious. The alternative is to use the JS console.
In FIrefox, you can open a given script that you've stored on your computer by pressing Ctrl+O/Cmd+O, selecting the file as you would in any other program, and then pressing Enter. (Note that this means you might need to press Enter twice, since opening the file in question merely puts its contents into the console input and does not automatically execute it—sort of a hybrid clipboard thing.) I have not tested the limits of the console input for e.g. input size.
As far as I know, you can also use the JS console to get around the design of the dubious WebExtensions APIs—by ignoring them completely and going back to the old days and using XPCOM/Gecko "private" APIs. The way you do is is to open about:addons by pressing Ctrl+Shift+A (or whatever), opening or pasting the code you want to run, and then pressing Enter. This should I think give you access to all the old familiar Mozilla internals. Note, though, that all bookmarklet functionality is disabled on about:addons (not just affecting bookmarklets that would otherwise violate CSP by loading e.g. an external script or dumping an inline one on the page`).