I've long been a proponent of site-wise distributions for metrics like this, but I think one has to limit this to extreme outliers. Whether one has to subdivide to be sure various brain regions are included or whole brain, I'll leave that up to you. You can help with the comparisons by using 3dUnifize to make datasets as similar as possible. Doing the comparison in standard space with a specific template will help too. Resampling to similar resolution may be useful. Like you, we receive and analyze data from many different sources, and there is certainly a lot of variety in FMRI data. So including partial coverage EPI datasets will be much more difficult. Please let me know if you have any more questions or concerns.
