The diode is most assuredly a Schottky and not a zener, used for reverse polarity protection of the MCU. But also it’s preferable to use a low pass filter for the MCU in FET drivers.
Here a classic FET+1 circuit (for e-switch here) : DEL's OSH-Park driver boards - #3 by DEL
R5-C1 is the LPF, 4.7R and 10uF
C2 is a decoupling cap, 100nF
You can probably save C2 by putting the LPF after the diode.
The diode can also be replaced by a PFET, when doing VCC voltage sensing (which you should do with a T1616 since that saves two resistors), there is no need to correct for the diode voltage drop since a PFET has virtually no drop. I usually use a small SOT-723 package.
PB0 and PB1 are good for PWM out, but PB2 and PB3 are not ADC pins, check 5.1 Multiplexed Signals in the datasheet page 18.
The standard flashing pad layout is UPDI - + with 1.27mm pitch.