If that's something with a lot of pins anyway (MCU, FPGA, etc.), probably just better to enumerate all of them, and toss the power sections off on their own sheets.
You can stack pins, but it makes the dot, and doesn't specify which footprint pins are actually connecting, which may be helpful to read. Yeah, outstanding problem, pretty sure I've voted for the bugfix myself...

Can also make a custom footprint, but this isn't really sensible for parts with pin counts this high. I do this sometimes for, like, single transistors. For example, the DFN/PDSO-8 footprints that are nominally 8 pins but 4+pad are literally the same piece of metal? Doesn't make sense to pin those differently. May have a few variants of those in case you run into, like, different gate/source pinouts, or I suppose there might be, like, regulators using the separate pins for whatever, and the rest as a tab, so they can't all be numbered 1-2-3 as they can for the MOSFET case. In which case you need a 1-2-3-4 and the rest 5 pinout.
Personally, that's as far as I prefer to go, as far as folding pins together in footprints, and keeping variants of them.
There's also the trivial-ish case, of unconnected pins -- I typically use '0' for unconnected (usually unplated mechanical) holes, of which there can be however many of, in a given footprint. Common on connectors with mounting pegs and such.
Also, incidentally, a lot of packages are made in a certain way, for example SOT-223-4 and DPAK-3 (4 including tab) where the center pin is physically the same piece of metal as the main tab; but this isn't always the case, as there are some LDOs for instance in SOT-223 where pins 2 and 4 are not physically connected! Read the datasheet carefully.

Tim