The B16 piston does use a larger rod- but that means that your stock rods won't have any clearance issues going into the B16 piston. You'll have plenty of room. The journals on your crankshaft will keep the rods in place so they won't slide around. If you look on most aftermarket forged pistons for Hondas, there's plenty of room for the rod to "walk" around on the wrist pin inside the bottom of the piston. You'll be fine.
Of course, you could always try to use CTR pistons too. The CTR pistons use the thinner rods, and they would take your compression up to 12.4:1 in the GSR block. Since you have the B16 pistons- just use those and be happy. It'll still be pretty easy to tune at that compression ratio, and you can run with a more aggressive set of cams than you would use with the stock compression and get even better results.