I'm no Matlab guru, but it is often ridiculed for how inefficient it is in solving problems. It is not compiled. I am not certain how much performance can be gained from MP or multi-core machines by default.
Anyway, if you are an undergrad, you won't need the Mac Pro to run your data sets through Matlab. However, if you have a programming background and are able to author multi-threaded data analysis progs then you should by all means get Mac Pro.