Just to update the above post, as it was me on the IRC channel "Brandon|i7" at the time..
In order to get Geoworks 2.0 apps to work I simply merged the contents of the GEOS20 folder into NDW, without overwriting anything. Starting NDW worked immediately as is, and allowed me to use all of the Geoworks 2.0 apps as they were installed. I will say this though, do NOT attempt to switch to Motif via the setup program. It lets you select it, but it will crash to an error and then you can't get out of it as the setup program won't even load. So do not attempt to switch to Motif. If your install of 3.1 already had Motif installed it shouldn't be a problem as the file wouldn't be overwritten. Mine didn't.
Performance wise, it seems strikingly similar on an 8086. Only just a tad bit slower on 3.1 vs 2.0. But it's very hard to tell, it's fairly decent actually. My main concern is that there's no launcher creator whatsoever in 3.1, which prevents you from making icons for your DOS programs. Most likely this won't be a problem though for every user.. To me it matters a bit.
Any questions you have I'm here to answer it. But I have to be honest, this is the best software I have ever used on an 8086!