FFmpeg comes with 'prores', 'prores_ks' (fka 'prores_kostya') and 'prores_aw'. Only prores_ks supports alpha channels (and the 444 & 4444 colourspaces) and has a few other flags you can set for advanced render settings. It's that's what I've used in the past for prores work. Which flavour of prores encoder is used in Voukoder?
"prores_ks" of course!