I agree with this. We should find some mission that we agree to use for reference, and use it. Something with known types of spawn that can be run straight through with a single ship, with little or no downtime to travel, and no interfernce from other players.
for the record, I think I have proved well enough, that my dmg is not dependant on others. and that is why ISE can be an actual good measure of dps. with multiple examples with multiple players you can pretty much prove, that a build is good or not for the purpose. ISE is a good test because everyone knows how it works, and people have actual parses on it, so they have a basis of comparison.
if we chose another mission, like you are describing, would just mean that the whole dps would mean less. yes we could compare the ship results to eachother, but not in real action where they were meant to be. also it would mean that to test the ship you would need to do something you might not enjoy or not as rewarding as a simple round of ISE.
I for one can say with confidence that ISE can be a good basis for DPS, if the results are treated with suspicion of the other players' present performance