Emulator load time inconsistencies are irrelevant, they don't effect IGT. Unless they do, which would be kinda weird.

This comes down to the accuracy of the emulator. As from the leaderboard rules:
All emulators are hidden for this game by default, as all emulators play this game faster than any console can, and therefore do not produce accurate results, or provide fair competition.
This means emulator and console are not cross compatible for comparison.

To answer the question a bit more simply; load times -do- impact and count to IGT for Gen 4 onwards