indeed they do NOT...i thought it was quite odd...had to reinstall as it was bugging me.The 13 and 15 inch 2015 MacBook pros don't have the same PCIe interface hence different link bandwidths. Its probably a bug in the system since you restored from a 13 inch to a 15 inch where the configuration is different and was probably an edge case missed in testing.
Only the sequential benchmarks suffered...not sure I could have told a difference just by using the machine and not benching it