Different design (Material 2 or 3 v.s. Material 1 mixed with Holo), different UX (e.g. multi-window v.s. dual-pane), Open source v.s. closed source, probably somewhat richer feature set from Total Commander (not entirely sure, didn't try it in depth).
Well this is so far my favourite Android file manager. I simply ignore the built-in file manager on all devices I use and pick Total Commander instead.