This is _precisely_ one of the things that VTT does. It has no graphical user interface. It uses Unix- like command options (you know, with minus signs). One other thing it does is to select parts of the file. If you ever wondered why the interlinear file has stuff like $L=A or $Q=T in each page header, you know once you've looked at VTT.
There's one frivolous option in VTT, which is to create output in RTF, such that the Voynich text automatically appears in the EVA Hand 1 font and the annotations in Latin.
I wonder if your tool could be made to invoke VTT and Bitrans, rather than replacing them?
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