You'd have to be bonkers to insulate the rafters without knowing what you're doing with the potential loft structure changes that may be necessary during a loft conversion. You might have to rip it all down.
In your situation I'd probably go for 200mm mineral wool between and 100mm PIR on top of the joists with your boarding loosely fixed on top. This is a good level of ceiling insulation with a non habitable room above. If it's further converted the PIR can be easily transferred to the rafters with the mineral wool left in place (there's some argument about thermal insulation between habitable floors; in my case we have empty bedrooms upstairs and I see no need to uncontrollably heat them via convection so I have insulation).
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