The rod length has nothing to do with displacement. The stroke and bore size are still the same as stock, the longer rod simply moves the piston farther away from the crank centerline.
The purpose of the long rod kit on that generation YZ250 was to reduce primary compression, increase crankcase volume, and increase piston dwell time at TDC and BDC. It did a good job of waking those engines up.
The rod is 5mm longer than stock. The spacer is 4mm, and the gaskets (2 of them) are .5mm each after being torqued down. The kit did not change the displacement, or the compression ratio.