If I am concerned about my theme being search engine friendly, how does TF handle this? Is it something I need to design into a theme myself, or is there anything in Themeframe that will help with this, such as handling header tags, etc.? Some themes and theme frameworks on the market are extremely good with SEO. What can you say about Themeframe in this regard?

A theme built with Themeframe is no more or less SEO friendly that say the TwentyTen default theme. There are many plugins to handle that function or you can as you suggested build it in yourself. Also IMHO SEO depends more about content.