Order of reaction / Rate-determining step in enzyme catalysed reactions
The rate determining step doesn't have anything to do with any of the factors you mentioned. It's not even true that the rate determining step can be determined directly from the rate of $$\ce{\mathrm{ES}-&gt;\mathrm{EP}}$$
The correct definition is that it is the biggest barrier from a stable species (reactant or intermediate) to any subsequent transition state along the reaction coordinate.

Your comment about the apparent rate of the reaction is unrelated. The rate-determining step is an intrinsic property of the reaction and its mechanism. It is unaffected by concentration, though concentration effects may change which mechanism out of several is predominant.