"First off should the 9500 also have a configuration including encapsulation dot1q . . ."
Possibly not. On the 9500, 1q encapsulation might now be the default (which Cisco does sometimes changes over the years) and/or Cisco's ISL might no longer supported (if the latter is true, there might not be any encapsulation choice, making assigning it, moot).
". . . should nonegotiate be added to disable DCP?"
Did you mean DTP? If so, I generally don't bother to deactivate it, but if you're not using it, deactivation is likely good.
"I also noticed vlans did not match as well."
Likely an error.
"What is the best practice for trunk configuration?"
Unsure I've ever seen "best practice" recommendations, for trunks, but likely they exist, although how "best" they are might be debatably.
For example I'm guessing @balaji.bandi might consider best practice explicitly allowing specific VLANs on a trunk, but I lean toward allowing all VLANs to default across a trunk.
Years ago, when large L2 topologies were the norm, and switches, and port bandwidths, not as capable as they are today, pruning unnecessary VLANs could be a worthwhile optimization. (Heck, even VTP supports an auto prune feature.)
If your topology is much more L3 oriented, you shouldn't have numerous VLANs "available" for crossing trunks, i.e. pruning by design. To me, mucking about with VLAN assignments, is just one more way to manually make an error (like, perhaps, your OP example).
Of course, another reason for assigning allowed VLANs is for "security", but if your security really relies on this feature, I would wonder about your VLAN usage and/or your overall security posture.
As I say, what's "best" is likely debatable. As there's not a whole lot to standardize for trunk interfaces "best" might best (laugh) be done considering what's best (another laugh) for your network.
BTW, whether I'm right or wrong about @balaji.bandi's opinion (only chose him as he already posted on this, and he's one of our VIPs - i.e. worth paying particular attention to his posts) on using a trunk VLAN allowed list, I'm sure he too could provide pros and cons, and considers whatever his choice is as "best" (which is perfectly fine).
