If you have a 44net subnet behind your router, machines that do not have DNS entries at ampr.org will not be able to reach BGPed networks, because amprgw requires any host passing traffic through it must have such a DNS entry.
At the moment, simply removing the default route in your ampr table solves this and routes those hosts vis ISP NAT.
By automatically creating individual routes for BGP subnets make this a little more diffcult, and breaks existing working setups. Even if this is not a big issue for people with good networking knowledge, it breaks things for those that should
have expected a simpler setup and are not profficient in networking, contrary to the initial goal of the proposal.
I think it is a little broader than this. When you have a BGP routed subnet yourself, and you run ampr-ripd in parallel to improve connectivity to IPIP-only subnets, you force the traffic to other BGP routed subnets via amprgw where they would much more efficiently be routed directly. (without NAT)
Of course a special version of ampr-ripd could be made that ignores those routes when some flag is given. You could release such a version and advertise its existence here, give everyone involved the opportunity to install it, and only then make the change.
Rob