Well, if you want to deal with the clipping, you've got a small number of possibilities.
To the best of my knowledge, no one's been able to add actual species client-side. What do I mean by "actual species"?
Part of a new species is the species number, which is used for identifying the species in certain ways. One of those ways is your character sheet - you'll notice most of the new species you play as are identified as "Human", and that's because their species number is set to 0, which is the "human" species number. This was a solution for an important number of problems, including the inability to image design characters beyond initial character creation. There's also some important info attached to that species number, like adding underwear and, near as I can tell, telling the client which appearance to use for clothing items. If a non-vanilla player species is picked, it defaults to human clothes but causes problems with ID. (Believe me, I played with a /lot/ of stuff on this.)
This species numbers are a bit of a phantom - I've been unable to find where they're enumerated in the client files (I actually mapped out what all of them are, but I can't find the list at the moment), which leads me to believe they're likely hard-coded in the client. The devs weren't particularly careful about species numbers, either; if you run around Mos Eisley Cantina using the %RT identifier in chat to pull species from targets, you'll find many of them come up Human (though not all) even if they clearly aren't.
So, with limitations in mind, here are the options we really have:
1.) Allow the clipping to happen. That's pretty much the approach I'm taking on Empire in Flames; some of the effects are pretty damn cool, while some are terrible.
2.) Disable wearables for species that are known to clip. Time-intensive to do because you need to test each combination, but mostly possible. Some of the races that aren't hooked up yet (c'mon, Timbab, where's my ACM editor?
) won't be able to wear /any/ headgear at all if that's the approach, including helmets.
3.) Edit the species meshes. There's a couple of ways to approach this, but basically it'd amount to resizing heads and/or flagging parts of heads so that they disappear to the degree it's possible. For example, if a Nautolan's head-tail things (I'm drawing a blank on the proper name) are flagged as hair, they would disappear under a hat/helmet. A few unreleased species (Timbab, where's my ACM editor?
) would need to have their entire head flagged, which would then vanish entirely with hilarious effect, but there'd be no clipping. Theoretically possible with the current Blender import/export tools from what I've been told, but difficult at best.
4.) Edit the clothing meshes to create entirely new wearables that are limited to /only/ particular species. Basically, it'd be Wookiee clothing writ much larger and more complicated. Again hypothetically possibly with Blender, but damn would that take work. In the end, it'd complicate the player experience - for example, when buying a composite armor helmet, you'd need to buy individually a "Togruta composite helmet" or "Cerean composite helmet" or "Gungan composite helmet" or "Nautolan composite helmet" or "Weequay composite helmet". You basically have created a lot of issues for crafters since they'd now need to craft some stuff specifically for certain species, since we can't just use the appearance datatable to point to the correct mesh. (Stupid species number.)
I'm lazy, so I'm sticking with "let it clip and the players will sort it out."
If any part of my explanation didn't make sense, let me know.