Does this support profiling of theme?

Yes and no.

P3 will break down performance by each plugin, the theme, and the core.

This is helpful for plugins because you can turn them on/off on a case-by-case basis. But since you only have one theme, the only optimization you can make is to switch themes.

If you want to compare your theme load times (in PHP), I recommend getting a baseline with twenty twelve, then measure your target theme.

If you want to compare your theme load times (browser), I recommend looking at your site with webpagetest.org. it will give you a full breakdown of how your site looks in a browser and a full list of performance recommendations.