@james @jon The cache auto-expires after enough time (weeks or months, depending on the host).
You have active .well-know for every combination of domain and subdomain I tested, but they're not all the same. All the jon@ Mastodon queries point to your bne account, which is expected behavior. Your sites all seem ActivityPub-compliant to me.
The only reason OP's suggestion doesn't work for you yet is that you don't have a non-ActivityPub landing page on the base domains.