Ffmpeg which entrypoints uses only supports a fixed input rate, so it will already be upsampling everything to the rate you set the encoder to be it can’t switch based on source, so adding on Roons resampling on top of that isn’t asking for the best results.
People seem to have managed external sources into HQplayer but I imagine it’s by something similar but not read it as I dont use HQ Player. Search the forum and you will likely find the thread.
And here it is.