As @Ric_ has just explained AD uses replication for resilience and DCs can also point at themselves. The fact that M$ have said that it is not best practice would make me question my design.
Also, if as you say "From the list of downsides at least half of those would still apply if you had two separate DCs with no clustering" doesn't that mean that you'd reduce the risk by 50% if you did have two separate DCs using replication?
Anyway, the genius that is @Ric_ has provided you with a good idea of how to fix the issues you are seeing. He's good with this stuff, I'd go with what he's suggested. If you decide to go this way, open a thread if you get issues and we can help.