OK.
You have more stroke so I don't know if it is the added stroke, the piston skirt design, or the Indy block.
I do remember the builder I ordered my pistons from (the smart guy between me and Diamond) told both me and Diamond to not notch the bottom of the bores so that the piston could have a little more skirt for stability. And it didn't hit the bottom of the bore/cylinder (block) with 4.250" stroke.

I have compared various pistons with ~1.32 compression heights and the skirt length can vary a bunch (2.38-2.755). But the transition from the piston boss to the skirt can vary also. Your experience taught me one more thing to consider when ordering all the parts. I just don't know if the KB cylinder liners for their low deck is longer than the Indy low deck.

I didn't see any clearancing at the bottom of the cylinder from the top, but the attached view when I did the mock-up at BDC seems to show a KB relief at the blue arrow?