I wouldn't swap the MOS figure with a shorter peg.
Personally, every figure I've seen where it was shortened, the figure's proportion looked off.
I think even Tony Meis who did this mod, eventually reverted back to the long pegs cause he said
he likes it better that way.
He has a very long torso, shortening the legs wont fix the issue.
It solves your issue of making him shorter, but now he looks like he has short legs.
At 1/6 scale, anything done sometimes can be magnified immensely, and something simple as replacing the foot pegs
makes a considerable difference.
When I had my HT Cap TFA, I had the short pegs, and Sideshow actually sent me the long pegs for free cause
some of the figures came with it, and mine didnt. Once I replaced it with the long pegs, it made a HUGE HUGE difference.
So something as simple as switching Foot pegs can make a huge difference.
The Crow's case, it makes it much nicer, but in supes case, putting a short peg throws off the proportion of the figure.
And much like myself, and most of the people, once you have it in hand, the height becomes a non issue.
It doesnt bother me one bit.