Off topic, but what about the XF permissions structure makes it unworkable for you?
I don't follow the issue with templates, maybe that's a level of structure that I haven't considered.
As far as the permissions structure, if you don't grant any special permissions to the registered group, and then have 2 "primary secondary" groups that are mutually exclusive, and then sub-usergroup "trees" that from each of those that do not intersect (no one that is part of "normal" can be a members of "club sub group 1" for instance) then that would function, permissions wise, exactly the same as if you made the "primary secondary" groups different primary groups as you have.
Node access is easily controlled.
Our club has paid members, a leadership team, a sub-group of leadership for voting members, another sub-group for elected members, node permissions for revoking viewing or posting rights to various areas of the forum, etc. I agree with you that it can get complicated. This is the first instance where I have heard that hamstringing the XF permissions system can actually cause an addon to not work as intended.