Of course you are starting the systems from a cold boot too? Your numbers don’t line up. I’m sure you are waking your MacBook Pro from Sleep which is very different from a cold boot up you are doing with your Mac Mini.
As far as disk performance are you using BlackMagic to compare? I think you’ll find the M.2 might be slower if you didn’t get the larger storage option. The number of Flash chips has a large bearing on how fast the storage reads or writes. The low end model only has one chip unlike the larger storage options.