a lot of the I/O circuitry which has found its way onto system chips just wasn't put on a chip with the CPU back then.

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Minor pedantry: the 6510 in the Commodore 64 (and its successor designs, such as the 7501, 8500, 8501 and 8502) has an on-chip I/O port mapped to $0000 and $0001 which is used for banking signals, essentially what the VIA is doing here, so such designs definitely did exist and predated the Mac. I imagine the use of a bog-standard 68000 was to stick with relatively off-the-shelf components rather than fab one with an I/O port, which Commodore (as the owner of MOS Technology) could do fairly cheaply since they owned their own fab and designs. The 6522 VIA is a pretty adept device, so it always seemed like overkill in this usage to me.