I don't think that is right. The subcontracted fee percentage is intended to capture the subcontractors fee element and your fee element, it should simply be added to the subcontractor quote.
If the subcontractor is entitled to those amounts under the subcontract then the fee gets added on top if they are not then they must come out of the subcontractor quote entirely (and the contractor should do that).
It really isn't for the PM to meddle in the domestic arrangements beyond ensuring that a proper price is given in accordance with the subcontract, the main contractor should not be using its fee to cover anything other than the subcontractors fee plus its own OHP etc that makes up its own fee element.
If the subcontractor is entitled to those amounts under the subcontract then the fee gets added on top if they are not then they must come out of the subcontractor quote entirely (and the contractor should do that).
It really isn't for the PM to meddle in the domestic arrangements beyond ensuring that a proper price is given in accordance with the subcontract, the main contractor should not be using its fee to cover anything other than the subcontractors fee plus its own OHP etc that makes up its own fee element.