Pin-out compatibility is the most likely reason, for an easy upgrade/downgrade from the -12 to the -45 variant for the 256-pin package. For the 381-pin package, it's from the -12 to -25 (not up to -45, probably for marketing reasons).
I haven't looked at the footprints to see if the 256 BGA and 381 BGA have common pins (so a common footprint could be used).
Thermal reasons could play a role maybe, just look at the number of IOs between the 256, 285, 381 and even 554 BGA. The very large 554 BGA has few IOs relatively.
But otherwise it's often just subtle marketing decisions.