I have now managed to get it exactly how I wanted.
I've got each browser in its own section, each with its own set of independent controls. Doing an 'Analysis' shows the results separately for each browser (even if the same category has been selected for all of them).
I really didn't like the fact that by default multiple (Mozilla) browsers get controlled by only one set of checkboxes for Firefox. For ages I thought that I'd made a mistake in my winapp2.ini because even after I had added Waterfox it did not show up anywhere in the main window or in the results.
It was only after ages of trying to figure out the problem that I realised the cache size results were incorrect for my Firefox install; it was way too big. I then realised that the "Firefox" result being reported was for both Firefox and Waterfox combined. It was only then that I noticed you can double click on the analysis results to see a breakdown of the individual files and, sure enough, there were items from both browser folder locations listed in the results.
Having multiple browsers all listed under a 'Firefox' entry is confusing (and inaccurate). That's why I wanted to use sections to separate them.
I therefore scrapped the idea of using winapp2.ini and instead switched to winapp1.ini so that I could make my list from scratch. I didn't want to do this at first because I thought that it would mean me having to manually recreate all of the other sections settings in addition to my own custom browser settings that I was adding. But once I found the ready-made default set of ini entries, it allowed me to still have access to all the built-in defaults, but in a customizable format that I could edit however I wanted.