1. Isn't per-project presentation tweakage a CSS problem, not an HTML problem?

CSS is a problem all by itself. But yes, you can do a lot of look-and-feel adjustment by first being careful to emit the right attributes so that you the right hooks to hang CSS on, and then tweaking CSS. But it's not a 100% solution, especially if you decide to do things like emit Javascript for dynamically sorting tables.

2. Per-project templates don't seem to mix well with global code.

I'll cop to a bias here. I used to worry a lot about cross-project code, portable libraries, building frameworks, and so forth. But the time investment never seemed to pay off. Now I worry a lot more about making things usable within a project. YMMV, but worrying about use before worrying about reuse has paid off for me.