Yes, I think so. But as r0lZ said, you can adjust the depth when BD3D2MK3D creates the 3D subtitles. At the options tab, you can specify an "Additional 3D subtitle depth". By setting a positive or negative value you can chose to make them appear closer or further. For me, it was a bit of try & play around with some values to see which would give a goodlooking result.
I once had a bad 3D disc with empty planes that I didn't want to recode. Fortunately, this video had a large enough black bar at the bottom. So I created a SUP stream that was positioned in this bar. It wasn't ideal, but better than subtitles interfering with video objects.
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