I'm not sure what you mean there. Inter-subjective verification by definition is the verification of something by two or more subjects or persons. If you and I were the last survivors on earth, we could indeed inter-subjectively verify things. Perhaps you meant to say, "If one of us was the last survivor on earth, and hence, inter-subjective verification was impossible...."
Sorry, I miswrote. I should have written you or I, not you and I. My point was that we could still do science without intersubjective verification, albeit not as well.
In my opinion, there would be no logical reason why methodological materialism would be imposed on a sole survivor. The survivor might choose to impose it on themselves, but that decision would not be logically forced upon them. As the sole survivor, he or she could simply redefine science as "Anything I myself can verify". That is, as based on subjective verification alone. Redefining science in that manner would be permitted because the only person he or she would need to convince of something would be themselves, and that would not necessarily require them to restrict their inquiry to methodological materialism.
But wouldn't that sole survivor be subject to the same methodological limitations whatever he or she believed? His or her science would still be confined physical reality whether anything more existed or not. Nothing would need to be believed or known for that to remain true, right?