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Yes, some will be transmission routes so while R is high they should all still isolate if they have been in contact with a case. The hope is that enough will be immune so the R goes down comfortably below 1 and all isolation ends.
But R isn't some magic number that changes and we just wait for it to be low enough for things to be cool.
R is determined by things such as self isolation, vaccinated transmission dead ends etc.
This is the point under question though isn't it?
If we are asking previously infected people to self isolate, presumably because there is a risk that they are not a transmission dead end, then why would vaccinated people be such a dead end?
(Apologies for the unfortunate use of the 0hraae "dead end")