Hi Jonathan. As far as I know, the intake of a KZ10B is always open and by the time the inlet starts flowing, the piston is already on its way up, getting out of the flow path. At TDC the piston is well and truly out of the way.
I've shortened the inlet side of kart pistons myself, but that was a reliability issue rather than a hunt for power, because sometimes the bottom lips of the piston skirt would break off, so I decided I'd better remove them myself before they could start wandering through the engine.
By the way, I happen to know that you're talking about a 125 cc TM kart engine, but not everybody here will, so try to be as clear as possible about these things.
And while you're at it, a brief introduction of your good self would be welcome (assuming you haven't already done that in another thread, in which case it's my bad).
There is no problem when the auxiliary exhaust portst are interconnected via the open piston pin because there is no pressure difference between them, so there will be no flow. And the same is true when the piston pin connects the tranfer ports with each other.
But in-between these two situations there
can be a problem, when the pin bores of the piston (the yellow circle in the picture below-left) connect the auxiliary exhaust ports with the transfer ports underneath them. This either limits the size of the auxiliary exhaust ports, or it necessitates plugging the pin bores (picture below-right) so that they are flush with the piston skirt as much as possible. Here you can also see that chamfered pin bores, while facilitating pin fitting, worsen leakage.

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