Will Lion updates be included in the App Store download?
The information page on the App Store shows:

Released: Jul 20, 2011
Version: 10.7

Therefore, I think it's safe to assume that the 10.7.1 update will have to be applied via System Update after installation.
EDIT
As of today, 23 August 2011, the App Store shows:

Updated: Aug 23, 2011
Current Version: 10.7.1

So, I guess the fixes are included in the download after all!