the includes should have package requires for their base application in every case, if you find one that doesn't, fix it please! (after posting so I can be properly embarrassed in public!)
the db_flush call should be fixed in 5.5.1 final (it's supposed to be db_flush_cache) ... hmmm maybe it didn't make it in before release.
No. It's on HEAD for 5.6.0, not 5.5.1.
You may want to edit that locally ...
I have noticed that if you pre-install some includelets before installing layout-managed-subsites you end up with a failure of the postinstall script as it tries to install them again.
Oh, wait ... I think this is due because the now-obsolete layout-subsite-integration package created the same three includelets (that map the standard acs-subsite application box + subsite box include scripts, and a third layout manager admin includelet) that layout-managed-subsite does.
As I explained in another post, layout-subsite-integration is obsolete now that we support package extension and should not be used.