Get a nicely configured MBP and be done with it.
It's the most common platform in research and academic settings for individual use these days, which means that there is a social dimension to the available support (i.e. people around you can help with problems). Meanwhile, the platform is narrow enough and the OS and hardware tightly bound together enough that one-off bugs and edge cases are exceedingly rare (which is not the case for Linux).
And Apple has very reasonable quality control in both hardware and software.
Having done a Ph.D. and dealt with the pressures and complexities that come therewith, I'd say that the overriding concerns should be reducing the PITA factor, keeping downtimes short, eliminating unexpected behavior and gotchas to whatever extent possible, and buying in to the largest on-the-ground support network (i.e. installed customer base) that you can find with identical hardware/software.
All of these things point to Mac for academic research settings.