Did more testing with some liposuction and force-feeding by altering unit.counters2.stored_fat between 1000 and 1000000. Also tried altering the (actual) strength attribute value.
Turns out that creatures with unit.flags3.unk1=false (old or young) also happen to be immune to size (physical_attr_tissues[0]) changes from alteration to muscle or fat. They can also walk around with an incorrect hacked unit.appearance.unk_4c8 and it doesn't change or matter.
Creatures with unit.flags3.unk1=true, which happen to grow properly, will change size within a few ticks, and their unit.appearance.unk_4c8 will recalculate to a correct value.
However, the flag is NOT the cause of the problem but rather another symptom. The evidence indicates that the size calculation function is being bypassed completely for some creatures, regardless of if they are growing or not. If the bug was fixed, all your old lazy corpulent dwarves would suddenly gain a few belt notches and move slower due to their increased size.
On another topic, the game appears to use unit.body.body_plan.unk15c and unit.body.body_plan.unk15d to determine if a creature has ANY fat or muscle in its body - it checks if the numbers are greater than zero.