Project Manager issues assumptions, however the Contractor does not agree to those assumptions as they feel they do not cover off all of the risks involved. The Project Manager will not accept a quotation with the risk priced in that the Contractor feels is needed - is there any way in which the contractor can challenge assumptions?
It depends a bit on the type of assumptions. If these are Project Manager assumptions that turn out to be incorrect, if these are then able to be reassessed as a new compensation event under 60.1(17).
If however they are merely stating that you should be assuming a lower level of risk in your quotation, and they make a Project Manager assessment accordingly, the only formal contractual way to overcome these would be through adjudication where you contend they have not assessed correctly (i.e. not included for risk which has a significant chance of occurring)