If a mech has one variant with 23k, one with 24k and one with 25k, its most likely that 24k is the normal value and the others have added/lowered armor to free tonnage or use free space.
If there are only 2 different armor values I'd use the more common value. If there are 3 variants with 24k and one with 23k I'd use the 24k.
If its a 2/2 situation... well, your choice, but I'd use the values of the prime in that case.
Ah, I did misunderstand you, didn't I?
You mean that both variants have 25k armor, for example, but one variant has more armor on the arms and one more on the torso?
In that case I would use the values of the prime variant.