I can't remember the 747-100s (my memory works in reverse - the more recent, the more difficult to recall) but the narrowbodies had standard configurations - 16/130 for the 707, 16/123 for the SUV and 12/99 for the STV. If the product planners wanted something different, it would be for a full timetable season but I don't think we had carte blanche, there had to be a very good reason for a deviation from the norm. I'm pretty sure the daylight Eastbound NYC-LON STV has a much bigger F-class cabin.
I'm trying to imagine: if LON-PIK-YYZ were the only year-round all-Y route, you could theoretically operate it with a singleton aircraft, but in practice you would absolutely need a second aircraft as backup - or risk regular substitutions by an aircraft with 12 fewer seats (on a flight that was usually full). Hence the availability for charters, extra sections etc. Plus the need to accommodate scheduled maintenance. I guess, over the fleet, a couple of reconfigurations would be necessary each season.
On occasion a STV would be reconfigures in all F-class for royal tours. Afterwards, it might be available for a week or so for ad hoc use. I can recall it being used for the daylight Eastbound, whether due to unserviceability or a heavy F-class demand (and very low Y-class - in which case indeed the lucky Y passengers would get the upgrade). It was also used on at least one occasion as backup for an u/s Concorde.