Lots of folks using Roon find that upsampling sounds better. Ultimately it depends on your DAC quality. Many DACs benefit from upsampling. It makes no difference for my DAC so I just set Roon to stick to native sample rates of the original file.
Jitter is a whole other problem. Either go for a DAC that reliably rejects all incoming jitter or use reclockers and try various fancy cables until you think you have a half reasonable working solution.