I have always thought about this in the sense of hanging a clock on a wall.
- 1:200mm is the parallelism of the clock (flange face) against the wall (stationary flange); hence, any diameter means applicable in any/every direction.
- 3mm maximum distance tolerance on 12 o'clock position (bolt holes).
I believe the clause was included to give baseline tolerances to help avoid induced stresses from bolting poorly aligned flanges together. I can't comment on why the clause may have been removed, however.