That's the point, it won't at all.
IIRC, with the exception of unindexed, the 'a' in 'a brown kitten' won't even be matched in the first place, so it won't get into the pass of tokenisation to match against phrases.
OK, search engine theory time. This is, broadly, how all of the search backends (except unindexed) work.
You start off going through all the posts, looking for sequences of words, a word being defined as multiple word-characters joined together. You store each of the words you find and the position in which you found them. Thus, you have your index - a list of words, a list of the positions they were in and the posts that contain them.
When you perform a search, you do the same thing: you break the search query up into groups of word-characters, before looking those up in your big list of words.
Matching words on their own, then, is simply a case of looking them up in the index and seeing which posts match the most words together.
Matching phrases is much the same except that you're looking for words in the same post and in contiguous positions.
This is how, ultimately one would match 'brown kitten'. But the 'a' will have been dropped long before it makes it into the index. Meaning that even if you could ignore the two-character requirement, there is no way to actually find it in the index, because it's not there.
In essence, when you search for 'a brown kitten', it's internally being parsed to 'brown kitten' before it gets thrown at the index.
Now, you can relax the rules around how indexes are built, sure, you can alter the criteria for what a word is and what 'word characters' are, how many letters etc. However, you need to go round and rebuild the index (which for any sizeable forum is a LARGE task), assuming it's even possible (MySQL FULLTEXT, I'm looking at you) and assuming that the word you're searching for is even going to be matched ('a' will be excluded by MySQL FULLTEXT even if you change the minimum word length there because of its commonality)
If you do decide to relax these restrictions, you will - guaranteed - have more white noise coming back in searches, for a vague and possible improvement to phrase searching. Even though it's still broken by the various mashing that goes on to deal with escaped characters, accented characters, inline bbc etc...