Is this when installed on a USB 3 external drive or on a USB 2 external?
Its not the USB device or port version that is the issue. Its the version of the OS. But I successfully used the InstallESD.dmg obtained from the Internet Recovery process to create both a 10.9 installer partition on a usb 3 disk and also installed 10.9 onto another partition. Both the installer and the mavericks os boot fine.
If Apple continues with the Dual Releases of Point Release updates for Mavericks I'm not sure any App Store version of Mavericks will ever be able to boot the newest Mac computers that come with the special build for the new hardware.
True. But what normally happens is that the newer device OS releases generally get merged back into the retail/app store version. Unfortunately you'll just have to keep trying each release until this occurs. Or do what I did above and get the right version from Internet Recovery.
To me it seems they have specifically targeted new Mac's to only run, boot, that new hardware from the special version, and updates to that special version, of Mavericks that originally comes on them. Only time, and when and if there is ever a 10.9.2 update, will tell.
I think its really a case of the app store version and previous versions of the OS not supporting the machine/hardware - probably the drivers of the newer machines haven't been added. So really the newer machines require a build of OS X 10.9 which support the machine. Without this it cannot boot from the files/installation. Again it doesn't seem to matter what device you are using (usb disk, usb thumb, even internal drive). If it has a version of OS X which doesn't support the machine it can't boot it.
Matt