If you scale a piston using the size atribute the base of the piston is fixed to the same position and the rest of the piston translates to that point
If you scale a piston using the tinker panel the piston is shrinked to the center, thus causing two pistons with the same aparent size be in different positions while having the same position coordinates
In the example you can see the two pistons are at the same Y but one is clearly higher than the other
EDIT: Other parts affected by this issue
ResizableWheel
LandingLeg
Fun fact:
Piston and LandingLeg use an atribute called scale while ResizableWheel uses size (in fact suspension, landing gear, resizable wheel, jet engine and rocket engine use size but solar panel array, landing leg and piston call their atribute scale)
@AndrewGarrison In the resize tool there's a tinker mode and a legit mode and the results are different for those parts because of this, I may have to find a workaround, I understand that now changing the attributes and the scale reference would break all the crafts