I consider this a bug. You know you need to check for update of an app at startup. You also know that app is marked for auto-start, and you have the limitation of not being able to update it while it is running. It's clearly a bug. You trip yourself and call not doing it a feature?
However I see something similar in the list of features for the future.
Delay apps set to autorun until after the updater has done a check, possibly not starting the ones that require an update
Problem is, this is actually a very annoying bug. I mean your apps start and are loading and then updater checks them, informs they have updates, your apps still don't show their main window so you click on next and get them to update, then your apps show up and the updater says it cannot update because the app is running.
So you close the app, update it, and manually launch it again. That's pretty annoying if it happens every other day, which happened to me during this week.
So here is an up vote and hopefully a severity increase or something, to get it up on the todo list.