RUSA membership is required to belong to any rando club which requires this concurrent membership for its own membership, such as mine. Therefore it is a de facto requirement by at least some rando clubs which run brevets, even though this requirement is not spelled out in the RUSA rules, as you point out. My club does not require club and RUSA membership for populaires, only for brevets of 200k and longer.

San Juan Cycling Club doesn't have a functioning website, so it's impossible to find out about their rules other than by phone calls. However, since the OP had to get an RUSA membership, I assume it's the same or similar.

I've never heard of a fee being required for a permanent, though I suppose it's possible for a club not to accept your card without a fee. And of course club and therefore possibly RUSA membership are required for the club to take and process your card for the permanent.

I've also never heard of an ACP brevet without a fee, though again I suppose it's possible for a wealthy club to simply waive the fees and pay the expenses itself.

One can certainly ride any brevet or permanent course at any time other then during an organized event, free of charge, solo or with friends, and just not submit a card or get credit for it. It's not quite as much fun, but it is at least as challenging, since there are no club manned controls or support at them. This is a great option for those who are attracted to these challenges but are repelled by the expenses.

Perhaps you could explain more clearly when and how you've seen fees charged and waived.