The issue is much more complex:
All the core Il2 bombs have a pivot at (0,0,0) BUT they are positioned so as, when they are aligned along their longitudinal x axis, with their pivot at (0,0,0), the upper border or their body is tangent to a line aligned along the lateral y axis, positioned at z = 0.1585.
This is true for all bombs and clusters - except the bomblets released by clusters which are centered on (0,0,0), no matter their volume.
Rockets are similarly centered on (0,0,0) no matter their volume, and also torpedoes (which is rather stupid but the whole issue of torpedoes in Il2 is rather crude).
Exception - the Italian bombs:
The bombs named bomb-50kg-it and bomb-100kg-it abide by the rule, as any other Il2 core bomb
The bombs named BombIT50Kg, BombIT100Kg, BombIT250Kg, BombIT500Kg, BombIT630Kg are positioned like rockets and torpedoes.
Another exception BTW is the FAB-2000 and FAB-5000 which are also positioned like rockets and torpedoes.
After quite a number of checks I got to the conclusion that when the SM79 was introduced, they needed to address the issue of vertically positioned bombs - but the reason was forgotten due to changes in the teams (1C-Ubi-TD) and we got these Italian 500kg and 630kg positioned as vertical bombs.
For the FAB 2000 and FAB-5000 that were introduced with the Pe-8 - it seems most probable that the issue is a lack of coordination between TD and the Pe-8 modellers