Workflow for creating / maintaining similar themes - best practice?

I’m doing well developing a new theme starting from the basic starter theme. I have most of the issues resolved, and will soon get to a point where the two themes I want to end up with begin to diverge. For instance, one will have support fro Adsense and the other won’t, but most of the basic structure, loops and styling will be the same. I could also see that if I was to develop further themes, my personal preference would be to start from something closer to what I have now than beginning from the starter theme. No offence meant,everyone has personal preferences!.

So, my question is, how should I proceed?

To be a bit more clear, at first, theme A might only differ from theme B by having a different single.html page, but both versions of single.html would have the same base, and it would be nice to change the base and have both versions re-generate while keeping their designed differences.

I don’t think master pages are the answer, but I may be missing something.

Any thoughts anyone? Thanks!

Not quite answering your question but might be useful Making a section optional (e.g. adsense or not)