Standalone SamD21 with Arduino Env PWM)

Hi everyone,
I would like to design a binary watch like this one : The Ultimate Binary Watch : 12 Steps (with Pictures) - Instructables
I would like to replace the atmega328 by an atsamd21 but I'm not sure if what I have in mind could work

I need 16 leds, so I've planned to use the pwm of the microcontroller (it has more than 16) but all are not wired on Arduino boards

So my questions are :
*. Can I use an Arduino bootloader (burnt with JLink) and use all the pins anyway or some pins won't be defined and the Arduino environment will be useless ?

*. I've found that each pin can deliver 3mA in standard mode and up to 7mA. Is that enough for one led ? Leds are always rated for more than 20mA but are supposed to be used with less than that right? (Depending of the amount of light emitted ? )

*. Can I use all pwm pins and which one is pwm capable? The datasheet is very unclear for beginners on this point. I'm not sure to understand, there is not enough timers but we can use something called TCC to overcome this issue ?

I can use a pwm driver like the pca9635 but I've not a lot of space on my pcb (everything should fit in a circle of radius <18mm)

Thanks a lot,

Guillaume