I wrote the little bit of additional code that will allow a consolidation to lock and run over the top of a checked out file today as part of my collection of locking fixes. Because the consolidation is changing data and not metadata, that trick works and the checked out file can come back on top of the consolidation. Server processes that change metadata aren't allowed to do this.
I checked out the root node of the consolidation tree and watched in the admin app as the consolidation process reserved it over the top of the check out, then released it when done, so that appears to work.
I am perilously close to done with this.
No thanks to Windows Server 2008 R2 which may be the most horrendous development environment known to man...