If you run an Advanced Segment where Keyword 'does not match regular expression' Tony's Baked Pizza does this filter any search term with baked in it or does the keyword have to include "Tony's Baked Pizza". Simply, I know, but I can't find the answer.
If I understand your question correctly, you're asking if filtering a whole phrase will affect the results of any phrase with a particular word in it, right? In that case, filtering the words "Tony's Baked Pizza" will not filter out any results with just the word "baked" in it. Of course, you can do that simply by filtering "baked" itself.
Well yes if someone search baked keyword then google will include your site depends on your site seo.