It's tough. Consider that when you're using AADS or AMM that enterprise directory stuff is required and the way some of those clients authenticate.
So, it's building the full Avaya tie in from MS-->Avaya and back to MS for configuration and authentication.
And the dial plan vs numbering in AD has to be consistent for the SIP handles it'll build - so, if you're "AD telephoneNumber 555" that'll make SMGR work with that number. If that's not a valid range in CMs dialplan or AAM or any other system dependent on numbering, you won't be having much fun.
And then you've got to have your provisioning templates set up so "when AD account X from group avayausers" syncs, that template would need to say "grab AD telephonenumber and associate with an existing extension of the same number on my CM and assign that CM endpoint profile to the user" and so on.
I've never needed to go whole hog on that and I'd be rather concerned. I'd lab the heck out of it starting from a reinstalled SMGR restored from backup on the same IP/FQDN and a separate AD to learn the product-specific and environment specific quirks.
How many users do you have to migrate? How attached are you automatic provisioning/deprovisioning via AD and letting the sync jobs to SMGR add and remove things? Without SMGR AD integration, nothing precludes presence federation from Avaya to MS so your Avaya phone off hook makes your MS chat status "on the phone", or your state to busy being set by Exchange to MS and passed to Avaya so when you're in a meeting, I can see your contact like that.
That all being said, I don't think there's a native way to query AD from a deskphone. Equinox and other softclients, yes, 96x1SIP, I don't think so... And even at that, you can pop in the AD IP and your credentials in one-x communicatior h323 and lookup dialable numbers and click to call them with nothing else other than client-side configuration to point to the LDAP server for searches.
They'll still be adding contacts from scratch from SM/SMGR regardless of whether they were created by virtue of AD sync or not. What exactly are you trying to accomplish? Do you need SIP phones or a useable company directory? Is the environment too big and tedious to keep the two consistent?