But somehow the files end up bigger than the original files, even when using the latest wavpack.exe instead of wavpackdll.dll built-in to XR3.
When I specify the options for the decoder (-hxl --import-id3) it doesn't behave like it does in PowerShell.

On the bottom left are the output files of XR3, on the right are the input files and the output files of wavpack.exe using PowerShell(seen on top left)

dBpoweramp also tells me that the sample size/rate of XR3's output files is 32bit/176,4KHz and doubles the original file size which means that it's doing some weird conversions.

Foobar2k confirms my thoughts as it doesn't recognize XR3's output file as DSD.