The polarity of in-process metal charging is irrelevant. It's the
signal position relative to what it travels over, where you'd
like the diode to sit, that determines the species.
Now, you might find special cases where it's better to use
a P diode in NWell, than a N diode in Psub - like a low current
bias line that sets PMOS current mirror racks, a capacitance
to Vss aggravates the PSRR more than a capacitance to the
Vdd where all the sources are referred (and, there is likely
also more opportunistic placement to be had).
But generally, "what works, for where you want to put it" is
the deal. These are "patch" elements, not operational ones
(unless you screw up).