No, adding the mod loader to the js folder won't do anything in this case.
I don't know much joiplay, but can't you edit files in it or edit the files externally on your computer then export them to joiplay?
Because even if you didn't use my mod loader to load the mods you would still have to edit some files to add the mods in.
For instance you could modify the "plugins.js" to add the data of the mods in the rpg maker format.
{"name":"TY_FnHFreeSkills","status":true,"description":"","parameters":{}},
{"name":"TY_FnHHexenMenu","status":true,"description":"","parameters":{}},
and then you could add the mods in the "js/plugins" folder.
It's up to you if you want to add the mods this way, but using my mod loader is pretty similar to the method above and maybe a tad bit easier since you only have to add the filenames only in order to load the mods.
Let me know if you got any other question.