I've been looking into other loaders mods, and I found that there's usually only one loader per tier, wich works as a non filtered miniloader until you actually set something for it to filter.

Could you do something like this with yours? I ask you this mainly because as it is now, when you want to upgrade your miniloaders, if you want them to be filtered, your current ones are not used, so you end up with a lot of them, having nothing to do with them

If you want to use only filtered miniloaders, then build only filtered miniloaders. It’s not possible to have them as a dual purpose entity, for the same reason the base game has separate stack inserters and filter stack inserters.