So, this is an interesting one. First, the author does not assign upgrade targets to the modified loaders. Therefore, even if I added support, it wouldn't change the behaviour – my mod ignores belt items that don't have an upgrade target specified. I also do not think the way they make separate entities (see more detail below) will allow the loaders to be upgraded without a very hacky implementation, since it is different entities but the base prototype data remains unchanged.
The second issue relates to how the mod author set that each configuration of the loader (w.r.t. the loader settings) is a different object. Why that is the case, you'll have to ask him. But that means that I cannot easily figure out what the loader related to a tier is supposed to be, or what tier a loader is supposed to be related to, since there are at least 4 different options in this case. I will continue looking at potential solutions for this, but I do not expect a quick solution, unfortunately.