So I have finally come to solution of my troubles, here it goes:
1. I was unable to switch off pan-scan. I finally achieved this by modifying bsplayer.xml, anulled this: <PanScanSV type="int">352</PanScanSV>
I am not sure if it could be somehow switched off normally, I tried various settings but I failed, so I had to resort to exploring and modifying xml.
2. I didn't realize that by switching to 4:3 ratio the pan-scan gets actually automatically activated and puts the videos in question to about -16%. How weird and how confusing for a user. Pan-scan change while switching to 4:3 should be indicated by OSD. Pan-scan should be indicated by OSD when a new video is being run too. Or at least there should be a setting for users to display that info in OSD in settings.
3. The videos were a bit confusing too, since they are screengrabs of 16:9 videos having upper and lower black border, which puts them to 4:3 ratio. This fact, added to point #2 above, completed the initial confusion.
4. There is still some very weird bug which lowers pan-scan when video gets repeatedly switched to/from fullscreen and/or aspect ratio changes repeatedly. This may result in video actually disappearing at fullscreen at pan-scan below -100%. With <PanScanSV type="int">0</PanScanSV> this is not the case (I think), but try to change that value and try again, that may trigger it I guess.