Until you design and solder up a PCB with $50 worth of parts, then discover the timers can't do what you needed them to do. (Ask me how I know). If you're a hobbyist, the STM32 has so much more functionality, and I've wasted so much time trying to get the underpowered AVRs to work, I'll never touch them again.
All of these chips have devboards in the order of $20. Surely you could have built a code prototype with a devboards before designing up a PCB?
In the embedded world, timers are very specifically designed. Yeah, TimerA is more flexible and maybe you needed more of that, but the less flexible TimerB on AVR is more power efficient (like 1/3rd the power or something). So TimerB has it's other uses. (Really, I'd say TimerB is specialized at frequency counting tasks but is less good at PWM or other "output" tasks. So TimerB is kind of an "input timer")
And TimerD is this weird behemoth that I don't understand yet. But someone probably used it for something good out there...
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But given the nature of TimerA vs TimerB vs TimerD (as well as the knowledge that TimerA is on different pins than TimerB), surely that should have cued you into the point that you should prototype your design?
Don't lock down your PCB until you have idea of what wires should go to which pins. And part of that process is deciding if TimerA vs TimerB vs TimerD was what you needed.
