For context, just over half of my planned experiments incorporate electrophysiological measures, and the rest don't - partly due to incompatibility between the electrophysiology lab and the type of measures and manipulations that are required in those studies.

The experiments of course are linked together by the overall topic (I'm investigating two variants of a certain phenomena), and the aim of studying those variants in parallel with one another which has rarely been done previously, and some variables are investigated across all the experiments (I guess you could say each experiment has the phenomena, together, and those variables plus something unique)

One of my supervisors' comments has led me to doubt whether the one completed and one-under-planning studies which do not incorporate electrophysiology have a place in my thesis - or can be made to 'fit' with the electrophysiology findings. This person is very much "not physiology=not interested" though...

Am I justified in thinking that content is a priority and that methods are to fit the content (and that illustrating the differences in methods/results is valuable too) and trying to be convinced that he is only saying these things because the 'other' parts of my work are not so interesting to him?

You will be fine as long as you can justify why the methods have been used or have been omitted.