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BD3D2MK3D will treat the subtitle file like normal subtitles and mux it, exactly like for Half-SBS. Of course, you are free to rename and keep the subtitle file also outside the MKV container, but BD3D2MK3D will not do it automatically.
With 3D subtitles, you must disable the 3D option for the subtitles in PotPlayer (3D Subtitles (Stereoscopic) -> Do Not Use (Recommenced)), because otherwise it duplicates what it thinks are 2D subs, and you get 4 subtitles! Anyway, I agree that the config of PotPlayer regarding the 3D subtitles is hard to master. To display the subtitles before or after the resize, I think that you should play with the Display Subtitles on Video or on Overlay (Alt-i) and the 3D Subtitles -> Subtitle Output After or Before Resizing options. For 3D-ASS, the problem is probably more complex, because ASS is a text based format, and PotPlayer has a lot of other options to let you position the subtitles where you want them (for example over the image or over the black border). You should select the option that does not modify the position encoded in the ASS file.
Personally, I don't encode in Full-SBS, so I don't need to modify the aspect ratio, and I don't know how the subtitles are modified by that option, but it should be possible to display the subtitles correctly. When I'll have some time, I will try to encode a short clip with subtitles and maybe I'll find a solution. But be patient...
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