Just a thought, but if you expand your thinking to include half par holes, you have 3, 3.5, 4, 4.5 and 5. So 18 holes is split into those 5 buckets, which works out to 3 or 4 holes in each one. Then the 3.5, 4 and 4.5 holes are mostly dropped in the par 4 bucket, with maybe 1 of each of the 3.5 and 4.5 holes slotted into par 3 or par 5 respectively. So you end up with 3 or 4 genuine 3s, 1 3.5 called a par 3, 2 or 3 3.5s called par 4s, 3 or 4 par 4s, 2 or 3 4.5s called par 4s and 1 4.5 called a 5, with 3 or 4 5s remaining. That works out to 4 or 5 3s and 5s and 8-10 4s.
I've never played any 6-6-6 courses so I don't know, but I would wonder if it was just that some of those half par holes are called 3s and 5s more than perhaps at other places. I think if there were 6 holes of less than 180 yards, I'd find that quite dull. Likewise if there were 6 holes of 540+.