First, this isn't entirely true, historically good ol East Frisia joined the HRE of their own free will after game start.
The ironic problem is that being a HRE member is FAR too good. Human players jump through incredible hurdles to get a piece of the HRE bonus action, while if AI were made self-aware every nation in the game under a certain size would be spamming diplomats and maybe gifts and marriage offers at Austria in the hopes of joining too, nobody in their right mind would ever want to leave, Italian AI would even reject the shadow empire offer unless they had a good reason to not want the 35 prestige hit, such as holding a fragile PU. Instead, I assume for game balance and railroading, AIs don't join the empire, members don't make an effort to drag provinces in, and in general AI aren't even thinking about getting any reforms passed unless they're emperor, despite all the benefits early ones provide.
Perhaps, and forgive me for saying it, the problem is that being in the HRE is too much of a net positive. Perhaps there should be penalties. Maybe HRE members should be charged extra for coring HRE provinces or annexing another HRE member vassal. Maybe some of that manpower being thrown towards the emperor ought to come at the expense of their members. As it stands, the only reason you'd ever want to not join (if you can) or leave if in, is, government rank? I can't think of anything else. Maybe a little bit of penalties being thrown at members, specifically penalties that only members face and not non-members attacking/annexing in, would better help with this whole HRE situation. A little bit of adjustment and maybe, just maybe, the HRE would actually stop being an ideal place for anyone who wants to blob, since it would actually penalize its own members for blobbing off other members more than it penalizes anyone else from the outside.