Hi,
<< I too get no "export alpha" checkbox >>
*attached the prores yuva 444 p10le profile.
** hope it's ok, I think this may be related, though I think you're right (the internal was there for the old one, but mine as you can see it "VoukoderPro" for both Format and Codec.
THANKS for this add-on!!
Sorry if I've done something wrong and not figured it out. But... I was using the old not-pro version of your amazing Voukoder. I switched to the pro version...
it's a bit more daunting regarding setting up the standard! but... all I want to do is export
ProRes 4444 with Alpha. 
Notice when YUVA 444 (16 bit, Alpha) selected in Type still no checkbox for Export Alpha. yes it's there for DNxHQ w/alpha, or PNG etc.
I did remove the IOPlugin old voukoder non-pro and uninstalled the old connector.
I started from the default video encoder ProRes KS, changed to yuva 444l10e, changed the format to 4444, and left the rest alone.
muxer defaults to mov, so I left that alone.
exports simply are missing the alpha (and are 75% of the size too )
See below:
1) selected first
2) 2 expected the export alpha - ok go to 3
3) open designer change video encoder to use yuva 444l10e (for settings see bottom image.) (I've re-created the Scene many times hence the discrepant name - but it's as attached )
WINDOWS 11, Resolve 18.6, Voukoder 1.2.1
here is the current "saved" profile.