Yes Man is there as a failsafe in the event that you botch your relationships with the other main factions. You should be able to do everything short of starting the final battle with any other faction, then switch to Yes Man at the last minute.
What implications does Mr. House's death have on the end game?
Answering the question exactly as you have asked it: there aren't any. What happens on the Strip and in Freeside at the end, all of that is affected by other quests and groups.