Good news - I've gotten most of the Standoff ships to work in WCP/SO, though it's a bit tricky (and there's a rather strange problem with the cockpits). Anyway, if you use Treman and set it to unpack only some of the files (option 3, I believe), and tell it to only take the files that start with mesh, ships, and mat (you have to run the operation 3 times, one for each), it will skip over that annoying little problem that pops up around 850. After that, copy/paste the folders into your WCP or SO directory, and use WCPEdit to swap them out. Then, do the same to the Data.tre file from the main WCP/SO directories, you'll need the tbtur.mesh file for the Broadsword/Crossbow/Sabre to run.
This is where the bit of annoyingness begins - with several of the ships, I found that it would start to launch, then CTD with a "Missing file" message - most of these were .mat files. So, if you don't mind having a little bit of oddity to the look of your ships (the Broadsword I pulled out of Standoff ended up with red guns on it's turrets), just copy a .mat file and rename it to whatever number came up as being the missing .mat file in the message.
Next, if you try to run with the Standoff ships in place of the defaults, it will say that you're missing cockpit/shipname.iff. You'll need to go into the cockpits folder (which should already be present if you're using WCPEdit), and copy and paste piranha.iff into the same folder - rename the copy to whatever the ship requires (Example: For the Broadsword, the copied file was renamed to bsword.iff)
Once this was done, I was able to get the majority of the ships to run - all the Confed capships (minus the Clydesdale), most of the Confed fighters/bombers, and a few of the Kilrathi ships. Most of the Kilrathi, however, would crash with a "mesh/ship.iff not found message", as in the case of the Dorkathi and Drakhri - in this case, we can't use those ships till Episode 2, at least.
Now, there's a couple of little bugs: The ships that use Particle Cannons in Standoff end up having Charging Mass Drivers put in place by WCP/SO...not for lack of particle cannons in the game, but I'm guessing because Eder and Co. used the CMD slot for their new particle cannon effect. Also, many of the ships ended up with Tachyon cannons - those two problems aren't huge, just swap the guns to the proper ones in WCPEdit.
The main problem I came across has to do with the cockpit - no gauges/frames/anything appear, and rather than being centered, the text displayed for comm messages is off to the left. The guns still shoot straight and look as they should, so if you've got good aim based on the center of your screen rather than a gunsight, you'll be fine.