OK the layout_managed_subsite_plain master is now set up and available when you install.
The only difference between it and the normal plain master is that when you navigate to an application, it will wrap it in the default page theme for the layout managed subsite. This gives a more consistent appearance.
Oh, and apparently I removed layout-subsite-integration from our CVS tree some time ago. Someone didn't update -P or otherwise was using an old checkout ... :)
Keep reporting bugs as you find them!
