I do understand that! For a Atmega328 the possibility is high that D4_INT is mapped to D3.
The atsamd21 is capable of PWM on every pin?! (I've no experience with atsam).
I will only need two dimmer and one switch port. So, if I wanted my board to be "MYSX compatible" which digital output pin on the MYSX do you suggest to use? As it is a mother-/daughter board design I'm working on the complete 2.6 MYSX is available.
I'm tinkering on a LED dimmer daughter board that will be able to get stacked on top of a atmega328p motherboard. The atmega328p motherboard is based on the layout (size, position of MYSX ..) of the sensebender gateway. The idea is, that the daughterboard may be used on top of the sensebender gateway if a mcu with more horse power is needed, for example for a combination of gateway & sensors. The atmega328p based board is suited for simpler tasks.