The clause at FAR 52.243-2 (Alternate V specifically for R&D contracts) is applicable only for changes specifically listed in the clause. Bilateral changes (supplemental agreements) are made separate from 52.243-2. The contractor would submit a change proposal, negotiate it with the government, and have it incorporated in the contract via modification. It's important to note that the Changes clause allows the contracting officer to unilaterally direct changes in the "drawings, designs, or specifications" of the research. The contracting officer must make a judgement as to whether such a change could have been reasonably contemplated by the offeror(s) at the time of award. If so, then 52.243-2 can be invoked. If not, a bilateral modification will be needed.