Looks like Media Encoder cannot use Connector Plug-in as Voukoder option is not available and due to this Media Encoder is choosing first available option (which is AAC) from the list.
Premiere Pro is 64 bit and due to unknown reason Queue button invokes 32 bit Media Encoder -> this result in problem, because Voukoder connector plug-in installed into 64 bit app folder.
So, temporary solution I've found - launch Media Encoder 64 bits manually, then push Queue button from Export Media dialog in Premiere Pro and task will be added into correct bit version of Media Encoder.