There's a text display bug in version 1.01 of RTM_TimerCalc. This bug doesn't affect executable code. It can confuse you if you're looking hard at the Timer details. Here's the story.
Mode-12 for 16-bit Timers is a non-PWM waveform generating mode. It's included because it offers a novel phase-shift able square wave capability. Selecting this mode in the dropdown display shows it using MAX -- which it actually does not do. Thus its a bug.
Here's a snapshot showing the problem -- click to enlarge.
MAX is the Atmel term for the Counter's highest value (in this case 65,535). But RTM_TimerCalc is not using MAX, its using TOP (the Counter value that forces a Clear). I messed up coding the Application. Then I missed spotting that error.
The problem is only a text issue. Its telling you about MAX when TOP is actually being used. I'll fix this problem in an upcoming release. For now, just ignore that text and have fun generating PWM code.