alanQuatermain: The version on the initial installation media seems fine:

codesign -vvv /Volumes/Pillars\ of\ Eternity/Pillars\ of\ Eternity.app
/Volumes/Pillars of Eternity/Pillars of Eternity.app: valid on disk
/Volumes/Pillars of Eternity/Pillars of Eternity.app: satisfies its Designated Requirement

After copying via the Finder to the Applications folder it's still ok:

codesign -vvv /Applications/Pillars\ of\ Eternity.app
/Applications/Pillars of Eternity.app: valid on disk
/Applications/Pillars of Eternity.app: satisfies its Designated Requirement

So, I'm inclined to believe it's the Preorder Bonus installer that's borking things.
Huh. Second time round it all worked. That's weird.

Was there a new copy of either the main game or the preorder installer uploaded?

alanQuatermain: I've been unable to persuade the game to launch here. I'm not sure if it's the preorder bonus installer that's breaking it, but the Info.plist no longer has a matching code signature, so the game won't run. Here's what the code sign tool tells me:

/Applications > codesign -vvv Pillars\ of\ Eternity.app
Pillars of Eternity.app: invalid Info.plist (plist or signature have been modified)
In architecture: x86_64

The preorder bonus installer doesn't touch the Info.plist, but it does touch Contents/_CodeSignature/CodeResources, which is where the digital signature for the Info.plist would reside. I'm thus guessing that's the problem?

I'll update with any further information I can determine.