At first glance, their patchDef2’s look the same, so it’s not that.
I guess it could be the extra interpolation to make patches smoother (which is built in because of how my code is structured, I’m afraid)
The z-fighting is because each map brush (or group, but Q3 doesn’t have groups) gets imported as a separate mesh, which is always going to happen when the original map just does smaller brushes overlapping large brushes. (Unlike the BSP, which basically combines visible brush sections into one coherent static mesh)
As for the lightmaps thing: UE lightmaps work completely different from the Q3 engine, in that you have a lightmap per mesh
Your maximum angle to smooth is… not a good idea, which might be influencing this as well.
That’s the angle between polygons that’ll generate a smoothed normal. 180 is basically opposite sides (which’ll generate a 0 normal, because they cancel each other out).
Anything much higher than the default 60ish is going to lead to behaviour you probably don’t want (since any sharp angle will become ‘rounded’)