MBPR 13" Late 2013. Two identical SSDs (different revs.) - one boots, one doesn't?
Stupid me! A fellow over at Apple Discussions pointed me into the right correction: Mac OS X 10.9.1 just doesn't equal Mac OS X 10.9.1.

The Mac OS X 10.9.1 on the external USB HDD had been installed using a different, older MacBook, thus just wasn't compatible with this MBPR. Back in the bad old days of Mac OS X Install DVDs, I was aware of the fact that there where different versions of the OS X Installer testing against the Mac ID to make sure that bundled versions gets only installed on those Macs which the DVD came with. And the DVD where clearly labeled in that sense.

Now in the days of Internet download and installation from USB sticks, SSD and HDD, one completely forget about this. On the other hand, with Mavericks being free, I don’t understand the need for such limitations, and not at least the recovery partition allows booting any Mac which supports Mavericks.

When you boot with the alt-Key pressed and you see at least one partition with Mac OS X 10.9.1, one just doesn’t understand why the heck the Mac doesn’t boot. Now I do. Apple would be well advised to simply add a short info line, like „This version of Mac OS X is missing components to boot this Mac. Please re-install from the AppStore using this computer“. It would take out A LOT of guesswork.

Anyhow… I booted the MBPR using the working SSD, installed Mavericks from the AppStore on the external USB HDD, switched the SSDs, booted from the external USD HDD’s now bootable 10.9.1 Recovery Partition, wiped the suspicious non-booting SSD and installed Mavericks. No further problems. Another option would be to simply boot into Internet Recovery Mode by pressing CMD-alt-R when powering up.