If you express it in a different unit system all E, m, and c will take different numerical values, but the relationship will still be true.
So there’s nothing special about the metric system. When we want to discuss this kind of relationship without reference to human convention we talk about a quantity’s dimension (not geometric like 3D). A Meter and a foot both have dimensions of length. c has units of length/time. 1 kilogram and 1 gram both have units of mass. And so on.