Mode-12 CTC returns in version 1.40 of RTM_TimerCalc. It took me a while to figure out how to make it work for run-time phase-shifts.
I hadn't realized there was a problem till I wrote code to scan the phase-shift across a range and back. That's when I saw it was 'flipping' phase angles 180 degrees! This was an unexpected and horrible result. I removed mode-12 CTC from version 1.31 and decided to forget it. One day a reddit user posted a question that got me curious. I did some extra digging in the Atmel documents and found the solution.
Version 1.4 will include extra code to make your phase-shifted square waves stay where you want them, even when changing phase-shift in run-time! Along the way, I discovered other 'advanced CTC' modes I'll share with you when I release this next version.