Note that HDR clips will usually have more saturated colors than their comparable SDR versions, and some movies also have different color grading in HDR as well, but it's possible something could be happening here.
There will likely be some inaccuracies in color, because of the way Premiere handles HDR source files. Premiere converts them to rec709 first, for display purposes. The format they use is okay if you want to use Premiere's own H265 HDR export, but for Voukoder, the gamma and color needs to be converted back to the raw ST2084-BT2020 data using my preset. Unfortunately, because premiere already converted it into a rec709 color space, converting it back is not going to be 100% perfect. While I do use accurate rec709 to rec2020 conversion calculations, you're going to lose a bit of the original wider color gamut, and there may be rounding errors in both conversions that create that effect you're describing. Gradation between colors though should remain just as smooth as the conversions happen in floating point.
Ideally, the best way to encode these videos with Voukoder would be to ensure Premiere doesn't recognize them as HDR to begin with, so it doesn't perform that conversion, and you can then output 1:1 color information perfectly (or as accurate as the encoder itself is anyway). One way I've found that can work with this is if you append the HDR video, to a video file that has the same resolution, codec, frame rate, and bit depth, but is encoded with rec709 instead of rec2020 metadata. Maybe encode a blank video with the same attributes, including audio codecs, and then use ffmpeg to concatenate the two files together. After concatenating, the output file will use the first file's metadata, so it will ignore the HDR metadata from the second file, and premiere will think the whole thing is rec709. Then you won't need the preset to pre-format the color correctly, as it will already be ready to export. If you can successfully get Premiere to ignore the HDR metadata in the file, you'll create a much more accurate encode in voukoder, but my preset should still get you pretty close.