I think you will find that they were a mix of both!
S1 panels were not drilled for trim,NOS door skins ive seen available are not drilled,but some NOS wings ive seen are.
If you have panels with existing holes,I would leave them as they are,as they will be so close to lining up,its not worth the hassle.
However,If you are of the meticulous,concourse, must be mm perfect brigade, then by all means fill them and re-drill them when you eventually get round to getting the panels all straight!! I am still trying "occasionally" to make mine all line up perfect after 7yrs!!
I have a mint set of S1 doors that one day will go on my S2,and I will have to drill them for the trim,and my spare,almost NOS, "fitted new on a resto project in the mid 80's but car never got finished" set of wings are S2 and drilled.