I'll preface these comments by saying I love these levels and the music that goes with them. I especially loved the music in Map01, which really set a nice yet somehow stealthily menacing mood.
Map01 has a few issues in Risen3D. In the area of Sectors 37, 41 and 65, a slice of sky texture appears. This is quite severe in Risen3D 2.2.09, less severe in 2.2.17. I also saw it in PRBoom-Plus 184.108.40.206. In both, it is the shape of a small triangle, thus answering to the description of Sector 65, which has a ceiling 2048 high with a sky texture, while the neighboring Sector 37 has a ceiling of 112 with a ceiling texture, and a floor of -1024 with a sky texture. I'm guessing these are trick or effect sectors, but I'm not sure what the trick is. This problem does not appear in Eternity or Chocolate Doom.
I'm guessing it's well known that the Map01 bridge over the nukage does not work at all in Risen3D, and shows a sky texture under the bridge in PRBoom-Plus. There are further bridge problems in Risen3D 2.2.17. The MIDFENC8 railings at linedefs 983, 1021, 1033 and 1057 do not appear, although the ZESSEL13 outer textures do. Not only is the MIDFENC8 invisible in Risen3D, but it also misaligns the METGRN03 textures on the columns in a weird way.
The last thing I noted with Map01 was the SSG secret/trap. I clipped into this area, grabbed the SSG, and then jumped onto the platforms on either side of the waterfall. I then jumped into the valley from the platforms, but by avoiding the waterfall, I did not cross the walking trigger that fired the trap. I had no idea there was a trap until I repeated the action and jumped over the waterfall instead. Even though this was designed with vanilla compatibility, and thus no jumping, it's worth remembering that some people will jump anyway. I see on the map that you considered this possibility by making most of the platform lines walking triggers with the same tag, but you forgot lines 3638, 3640, 3423 and 3424.
Thanks for these levels. They are real beauties, and I love the Quake2 look. I'm currently paused on Map06 after getting killed by an Archie. I'll resume playing as soon as I can. I also haven't encountered any issues in levels after Map01.