To answer the part of your question regarding number of finishers: if you don't count USGP in 05 (shudder), sub 10 finishers hasn't happened since Monaco 1996, but only top 6 scored back then anyways (but only 4 did finish, so this is an example of a time when just finishing would score points). It's very rare to have fewer finishers than points, I think besides the two I listed, these are the examples:

finishers year GP

5 1966 Belgian Grand Prix

5 1968 Spanish Grand Prix

5 1968 Monaco Grand Prix

5 1970 Spanish Grand Prix

5 1982 San Marino Grand Prix

5 1984 Detroit Grand Prix

Also some fuckery with the 1966 Monaco GP but that's a long time ago and I'm not sure it's relevant to your original question

Should they? It was kinda fun tbh, gives an interesting twist

Alternatively, why do these penalties carry over? If a driver gets a time penalty and retires before it’s served, the time penalty should be moot.

I was hoping so bad for a safety car so we would all have to wait for Perez to run 26 laps to unlap himself.. No skipping that part since Hamilton/Verstappen debacle a few years ago...

I was always (apparently wrongly) under the impression that if someone touched a car, that it could not continue to race. I assume this must just be for marshals, but could be extended to pit crew.

In my opinion I don't think a fix is necessary since this situation won't happen often anyway.

What I see as a much bigger problem is the 5sec penalty. Because most if the time 5sec won't actually change anything for the offender if they can just drive ahead 10, 15 or even 20 sec in a spread wide field. They should out harsher penalties like lost positions after end of race or maybe to get only half of the points if the finished position or something like that.

Couple of things they could do:

All penalties must be served on the lap they are given

Maximum pitstop time

Remove time penalties and make it a points penalty