The more I watch at it, the less I'm convinced.
The difference in dimension between the mekugiana is something that puzzle  
me.
Usually multiple ancient mekugiana have roughly the same dimensions 
 
 
 
 
but even ancestral blades mounted in Shingunto are not different :
http://www.h4.dion.ne.jp/~t-ohmura/gunto_023.htm 
 
and Shinshinto handachi mounted swords (Handachi is an Edo period mounting similar to Shingunto, with Sarute) are similar in placement but still with the
same larger dimensions in the holes :
 
This last has not been shortened. I'm sure because it's mine.