I am looking to upgrade the lower headset bearing on my BMC Teammachine and am wondering what everyone’s thoughts are on using non-OEM height bearings. In this case the standard bearing is 7.5mm, but there doesn’t appear to be much available in the upgraded category at that height with the required sizing. Multiple companies say a 6.5mm height would be fine, but in my mind a 1mm difference seems like it could be a lot.
Anyone have experience switching to a shorter bearing?
The trick with headset bearings is fit and proper adjustment. Better tight than loose. I would not substitute a different size or type for the headset. You don’t want any movement in that system.
Having said that, headset bearings do very little spinning and they would be the last thing I’d look to upgrade! 
Looks like the bottom bearing is a MR019, but I guess the question we need in order to answer your question properly is what are you looking for in an upgrade? Are you looking for a stainless version, solid lubrication version, etc? We need some more info.
To answer your original question though, from a mechanics standpoint I would not change the height of the bearing. You are likely to run into rubbing issues with the frame and fork.
Something with better seals is the chief reason for an upgrade, with the hope that I can stretch out my service intervals. It’s not something that’s difficult, I just find it annoying.