The Mastering Engineer wants you to record the best possible sample rate possible just so you can give him the best audio possible. 96 is higher quality than 48 but will take up more space on your computer. I'm not sure if I could hear the difference but plenty obviously can. It's a matter of your priority.
If you have the luxury of recording at 96 khz you may as well use it.
I would say that the difference between 48 and 96 khz is much less than 24 bit to 16 bit. That said, I would recommend recording at 24 bit all the time. And raise your sample rate (kHz) as to how much performance and disc space you have.
Hope this post makes some sense! There's no rules for recording but these settings have a direct correlation with sonic fidelity. The higher they are, the clearer your audio should be until a certain point that isn't as audible.. But then again your crappy snare will sound just like crap as it did at 41khz.