I have added the new config option anyway. But IMO it is useless as the aspect ratio stored in the MKV header should normally be the output aspect ratio (16:9) regardless of the full or half encoding. Anyway, if you prefer to use the full source AR, it will be possible to insert it in the mux options file automatically.
I did just a test with the new version of BD3D2MK3D, but there is still a desync problem with the 3D subtitles. I have to work again on that problem, and I'll release the fix as soon as possible...
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