A lower bound of O(n^2 log n) has been known for quite some time. Good luck going any tighter than that... https://eccc.weizmann.ac.il/report/2002/012/download/ [pdf]
However, yes, there are big differences based on the encoding. Nobody would accept using unary input encoding to artificially inflate the size of the input. It's also why the time-compelixity of prime-testing is sometimes confusing.
edit of course wikipedia links to a explicit lowerbound which is kind of useful for small cases. https://www.sciencedirect.com/science/article/pii/S0885064X0... has it as 2*n*m+2*n-m-2 which is 53 for m=n=5, which is not super tight, but tight enough to say that no 5x5 formula is ever going to lead to an asymptotically faster MM algorithm.