The schematic details are hard to see because of resolution, but i think i see some caps (100nF/10nF?) on every I/O pin? I think it drastically limits the use of such pins, by changing the pin capacitance. If you want to drive a fet with that pin, or generate a step signal, that cap would change the waveform perhaps not in a good manner. Also i cant see the diodes type, i assume zenner (or transil?) but which type exactly? I assume are meant to add 5v tolerance, but usually have to check the Vbr which depending on parts it could be like 10-20% confidence, and it may get lower than vdd, so have to check that out, and maybe leakages. I am saying because i think all those change the pins input properties and sometimes its good to have a pin with low capacitance, or without increased leakages. Just saying.
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