May be I am confused. A 'stroker' crankshaft has a bit longer throw(radius) on the rod journal. It will travel in a longer circle.
If you change the crankshaft, the piston and connecting rod are GENERALLY also changed. In most automotive designs, people do not shim the cylinder head, or much around changing the block when a stroker crank is installed.
The rod & piston, if left the same, WILL push the piston higher and lower(also further fore and aft) as it moves.
The rod comes installed on the crankshaft when it is assembled. Unless you are getting a kit that you press together yourself(good luck with that, a couple dial indicators seem necessary).
I would expect that the connecting rod installed should be designed so a standard piston(I know of no stroker 'specials' on the market) should be installed, and the piston would travel from BDC to TDC and stay within the bounds of the cylinder.
If you are uncertain, contact the vendor. If the vendor speaks a different language... try the TRANSLATF function to communicate your concern.
Off the top of my head, I would expect the con rod installed to be shorter in length, center to center between big end and wrist pin diameters. I dunno how else it could be, though wrist pin placement within the piston can be modified also. I'm sure you will get comment from someone who has mucked about with these.
tom
Added... I stand corrected. I looked at racingplanetusa web site. The Naraku indicates standard length con rod installed.
That means the piston would extend past the top of the cylinder at TDC unless the install is modified. A different piston could keep the same deck height, and leave the cam chain geometry unchanged from factory.
I poked around a bit more, and did not find anything from Naraku that would enable use of their stroker using a modified or specialized piston. Kind of leaves things totally to the customer.
tom