Commissioning using generator

That would be extremely unusual. You also call it an "emergency" generator, and often they are not what is called duty rated. They can run for extended periods, but are not intended to generate power for beyond typical emergency situations. If a generator is to be used for co-generation, or as the main source for the building, it would have a different specification and built differently. Now, the emergency generator system should be tested, that is for sure. There are many times that the transfer does not result in the outcomes desired or required. It is important to find this out before there is a true emergency. So, my recommendation would be to do all testing of all systems under normal power. Test as many sequences related to emergency operation (under the generator) as you can without using the generator. Then organize and manage a true blackout test. Cut the utility power from the building and test that all required operations are transferred and functional. All hands should be on deck for this kind of test, and it has to be planned very carefully so the right people are on site to ensure there are no issues that cannot be addressed immediately.