This has bugged me for years, but I couldn't quite put my finger on exactly what it was. Playing the first part of Surgical Strike just now, it was easy to see that many ceiling pits don't line up with their floor counterparts.
I decided to do a compare between CSBWin and RTC to see exactly the difference. I was very surprised. Not only are the pits out in several places in RTC, the graphics are very different.
Firsat, RTC's floor pits don't have the lip around the edge. The very central front pit has far corners that don't line up with the verticals.
Second, in terms of position, the worst offenders are the first row ceiling pits, left and right -- they are too far off the screen and need to come towards the center by 28 pixels. The angle of the edges of the second row centre floor pit is wrong. The right and left centre floor pits in rows 1 and 2 are too close to the middle -- they need to go further off screen. There are other minor discrepancies.
Have a look at this anim to see what I mean. You'll see the spacing between pits in CSBWin is consistent and perspectively correct. RTC isn't.

I'm curious to know which version of the game you got the pit graphics from George? Would it possible for you to modify the positions to more closely match the original game, and to put back the 'lipped' floor pits? I can provide them if you like.
EDIT:
I checked my archives and see that your images come from the PC version of DM. Another small difference is that the floor fades sooner in CSBWin and in conjunction with the better pit graphics, makes for a more pleasing effect. I guess FTL took the opportunity to clean this stuff up in CSB. It would be nice for RTC to also look as good as possible.