ROF2 is the recommended client but you can use Titanium, Underfoot, SoD, SoF, or RoF2. There are differences with each client, including bugs and kinks between zone versions, zone lines, etc (of which most of these issues are discussed on these forums). It's just one of those things you have to work out when you decide to run a server. For instance my server runs on RoF2 but uses the older zones. Most of the new zones have combat disabled, so if you want to use them you need to enable it (simple).
I think EQEmu just follows PEQ development so they really don't try to accommodate what 100 other servers might be doing, but rather providing them a platform to make said changes.
https://github.com/EQEmu/Server/wiki
Also, the github wiki replaced the other wiki like a year or two ago. So it's information is more relevant.
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