Look, being one of those people who feels the need for an owner group, allow me to explain things from my side of the fence.
When you look at the names to groups (Superadmin, admin, user), it leaves a lot to be desired. Theres little room to fit a rank between SA and admin, and what would you call it anyway? semisuperadmin? MegaAdmin? AboveAdminButNotQuiteASuperAdmin? SuperAdminThatCantTargetTheOwner? These are all rediculous names, and so the logical solution would be to create an Owner group, above SuperAdmin. Then you have room for CoOwner, etc etc etc.
Now, naturally yes there will be some pitfalls from this. All things have a downside. It's to be expected.
In this case, other mods that rely on the user group directly rather than IsSuperAdmin() will not target the owner (although any coders that do that should look up Compatibility and Redundancy in the dictionary)...
However, this is ultimately an issue that needs to be addressed in Garry's Mod itself. There should be a rank for Owner, as in a realistic hierarchy, you dont just say "Aight, Im top dog, these guys here all have the same powers, and you lot that are left are just users". No. In a realistic hierarchy, you would have something like an Owner, a Co-Owner (if applicable), A few Head Admins (aka Super Admin), then your regular admins, then your moderators that have only the essentials and nothing that can be abused, then your players.
Thats how a realistic hierarchy works. And garry cant say "That will work for you anyway" because all he has to do is turn around and look at Facepunch. Is facepunch sorted by "Garry, admins, non admins"? No. Its sorted by "Garry, some guys that can almost do garrys job when he cant be bothered, admins, mods, donators, users, banned users, spammers".
So when it comes to it, the 3 standard groups do not cover 99% of realistic server environments. Yes, it works perfectly fine in LAN parties, Listen servers, and other constantly monitored situations, but when you get around to say having a dedicated server, or a large community (HellsGamers, KickAss Servers, GMTower), you need to have a finer control of who is where in a hierarchy.
Granted, ULX does this anyway, but there was a time, and not too long ago too, when having ulx do this for us just wasn't enough.
Take for instance DarkRP's FAdmin. Just a few weeks ago DarkRP was updated to include immunity levels. Without these, you couldn't make an Owner group that could target SuperAdmins. But you needed to make the same group in FAdmin as you did in ULX in order to have any powers in either mod.
I guess what I'm trying to say is that when you look at things straight forward, yes, you do not need an Owner group, but in the real world, with a real hierarchy, you need to be able to take command over your staff, so people know what their place is. Otherwise you could get SuperAdmins challenging the authority of the owner of a server and causing hassles by terrorizing the server and banning the owner.