Back to My Mac registers services using loopback interface IPv6 address

It sounds like what you're really looking for is Wide-Area Bonjour (henceforth "WAB"), which is a system where Bonjour-capable clients, in addition to registering their services on the local network via multicast DNS, also use Dynamic DNS Updates (the scheme in the process of being standardized by the IETF in RFC2136), to register not only their IP addresses but also available service records with a traditional unicast DNS server.

See dns-sd.org for instructions on how to configure your Mac to use WAB. They even have a System Preferences panel you can download and install to make it easy. I believe they also have instructions for how to configure WAB to work with some well-known dynamic DNS service providers that support it, such as dyn.com (a.k.a. dyndns.com). If you run your own DNS server somewhere, you can also find instructions on dns-sd.org for how to set up your DNS server to act as a WAB server. For best results, it may need to be running BIND.

Using WAB-supporting dynamic DNS services, or running your own WAB-supporting DNS server, are your only choices. iCloud's BTMM servers do not support full WAB.

Back to My Mac makes use of some of the software infrastructure of Wide-Area Bonjour, but the iCloud BTMM servers don't provide full WAB service, just the parts needed for the particular way BTMM uses it. As you discovered, BTMM client machines put an IPv6 "unique local address" (ULA) on their loopback interfaces, and register that ULA with BTMM's servers. Connections between those ULA's are handled by IPsec-secured, typically IPv6-in-IPv4, tunnels between your BTMM Macs. It's intentional that you cannot connect to those services directly. This forces the connections to go through the IPsec-secured BTMM tunnel. The BTMM software on your Macs handles authenticating your Macs with BTMM and using that to make sure only machines signed into your own BTMM account can establish the BTMM IPsec tunnels.

Update: A couple more thoughts:

• Make sure you don't have "Block incoming connections" checked in the IPv6 settings of your AirPort Base Station. (Note that AirPort Utility 6.0 doesn't currently have IPv6 settings UI, so you'll have to use AirPort Utility 5.6 or earlier to check this.)
• Can you ping6 your home Mac's publicly routable, non-temporary IPv6 address from the other site?
• Does a typical BTMM connection (i.e. over IPv4, from another Mac signed into your same iCloud account, with BTMM enabled) work? Why are you specifically trying to make this happen over IPv6? I might be able to help you better if I understand your goals and constraints better.