Most modern ecu's really don't care about a different exhaust, they simply adapt. And many can get remapped to delete immo and other not needed features while releasing more power.
If you have the ability to make the standard management work correctly i would always recommend that for a standard engine. That way you retain all the thousands of hours of standard mapping, for instance for cold starting. It will fire up and run perfect in heat and cold or even up a very high mountain.😉
If going for outright power and if other modifications are planned for the future a fully programmable ecu is the better choice. Also ecu's from before the late nineties are usually less capable or there is less support to get them mapped. Changing to aftermarket ecu is always better then.