As always, the answer is "It Depends". 

For GSA/VA Federal Supply Schedules the answer is yes; they are purposely negotiated and issued that way.  Same holds true for authorized GWACs, the base contract stipulates agency specific clauses may be included.  The contract holder can certainly voice their objection if they so choose... that is why unilateral orders placed against these types of instruments are not authorized.

For other multiple award contracts (or FAR Part 13 BPAs) that are not available to all federal agencies, they would become binding if they are added and the contract holder accepts those additional terms and conditions.  Again, we assume you are referencing a scenario where these provisions/clauses are included in YOUR solicitation.

If you are going outside of DoD, an Economy Act Determination would need to be done first. I think that is beyond the scope of this question so we will not address that here.