Re: prehung door: flush w/subfloor?
The jambs won't be cut for the carpet, but should be cut for the hardwood. If both surfaces are being installed by the same crew, then yes, they should cut the jambs as necessary.
The thing is, you're asking about prehung doors, which indicates that you have not installed them yet, if this is the case, you can set the frames higher in the opening to accommodate the flooring, this will also save you from having to cut door bottoms to maintain an air gap of about 1".
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