Hi
"I suspect that what Apple have done . . . is to switch to DNS hostname as the primary name resolution method"
You may or may not know this but Macs are first and foremost multicast unlike PCs which are unicast. Macs will always try Bonjour (.local) first and then move onto DNS, TCP/IP and whatever else is in the network stack. Hence the reason why you should avoid basing local/private DNS services around a .local TLD.
You can't change a Mac's multicast nature without hobbling/breaking the OS in a major way.
". . . meaning that DNS must be in good standing"
Especially so with Macs but should be the case regardless. As we know PCs are a lot more forgiving and less sensitive to sloppy DNS than Macs are although even Microsoft with Windows7 and now Windows8 are fine-tuning this even more that these newer OSes are not that dissimilar to OS X.
"I . . . recently resolved an issue . . . preventing Macs from registering in Active Directory DNS . . ."
To be precise Active Directory itself does not 'do' DNS. The Windows Server that's presumably acting as the Domain Controller is. One of the 'problems' most network administrators have in dealing with Macs on a network is they (wrongly) assume the macs respond to it in the same way PCs do. They don't. PCs are DDNS (dynamic DNS) aware on the forward pointer. Out of the box macs are not. They're DDNS aware on the reverse pointer. What this means is if an IP address has already been handed out to a PC on the same network then the DNS service will assign that PC an rDNS record in the reverse zone for that subnet based on its local name and appended domain name. If the same IP address is subsequently handed to a Mac it will use the existing rDNS record that's already there.
If the PC is named laptop100 and the Mac is named iMac012 the rDNS record won't be updated automatically and the Mac may/will have an identity crisis because it can't resolve itself correctly. Namely it's name may resolve to its IP address but its IP address wont resolve to its name.
This can and does cause problems when binding macs to Active Directory as well as result in (in some cases) incomplete or failed logins that are random and seemingly difficult to fix.
A number of ways of stopping this behaviour is to either create static entries in the DHCP and DNS services for affects Macs or alter the default scavenging interval for stale records in the DNS service. 1-2 days usually works for me.
There are other effective ways of accommodating Macs on a 'Windows' network but the above do work well in my experience.
If Macs end up with multiple names there is a potential connectivity issues when using ARD. I've seen the problem posters are reporting on this forum since 3.7's release in earlier versions for this very reason. Granted 3.7 does seem to be more sensitive to network instabilities caused by sloppy DNS/DHCP than previous versions but hopefully Apple will provide an update soon that stabilisies this version to the level of previous ones. None of us have any way of knowing they will because Apple have always been consistent in never letting anyone know what they're planning with anything they do.
HTH?
Tony