Thanks, it's fantastic knowing that you found it all interesting enough to be worth spending that time on.
You're not missing anything with the ending - Yaldukra being there is what's different. After that extra scene is done, he appears in several scenes in both the Upstream and Downstream endings that he'd have been absent for otherwise.
Sorry for any miscommunication that occurred there - without spoiling anything in that initial post, I was trying to make it clear that the scene would have a further effect, but not that its main purpose would be to change the ending.