Can't speak for others, as I don't dismiss it. But seems to me in comparing the top teams, the records against each other would mean more than anything. Not end all be all as you are right.....doesn't matter what happens in reg. season.
Agree to a point that comparing the top teams means more. After all, they are the biggest threat to each other in the playoffs. But you can't automatically discount the rest of the teams in the conference.
If the Western Conference has better teams overall, then there is also more opportunity for top teams in the East to be upset by lesser teams if they are playing a Western Conference or even balanced schedule.
If there are additional losses, that can effect seeding.