I have to second the idea of using special codes. Of course, this depends on how well this software can read them. A right and left page card would be nice for auto rotation, I'm not sure how a b/w or color card could be useful with something like ScanTailor, but I imagine people are thinking of using this with other solutions. I know we've talked at points about manually writing ScanTailor config files, if I have time I'll look into it since I can easily do that (Java was my first language [what a shame, huh?]).
On another note, I've been using this software for a bit and the Java QR-code version is much more robust than the checkerboard alignment, and it is really pretty quick. Also, you can multithread this from the command line (*nix) thus:
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java -Xmx512M -jar ~/Downloads/qrpc-1.4/qrpc.jar ./Left > left.log & java -Xmx512M -jar ~/Downloads/qrpc-1.4/qrpc.jar ./Right > right.log && echo "done"
I don't think Java does any automatic optimization for multithreaded processors, so this will speed things up.