(What follows is my opinion and no sources)
You may as well ask the same question for "shehakol nihyeh biDvaro" - Why do we talk about G-d creating with Words for things like eggs which clearly come from chickens, or Oreos which clearly come from the Oreo factory? (Ok, it's possible that Oreos come directly from G-d.)
A bracha is meant to remind us of G-d's role in creating the world as we know it. We only touch the results of G-d's work (life as it currently is). Brachot are there to remind us of what went into that and how G-d touched it. In the case of ברא, we are only talking about living things, and I think the life is what G-d created ex nihilo. Bread is constructed of ingredients. Life is created.
New Life as ברא
In the case of borei, we are reminding ourselves that though we planted that tomato ourselves and watched it grow from a seed, we had very little to do with it. G-d created that very tomato life just as much as G-d creates fetal calves' lives and fertilized fish eggs' lives.
New Type of Life as ברא
If "a new life" is too "yatzar-y" for you (and as a parent, I would argue strongly with you on that point), let's go back further. G-d created the first tomato whose seed created this tomato. So this tomato is simply a reflection of the first tomato G-d created.
[Insert aggadah about G-d's diecast that makes different patterns.]
Life Itself as ברא
If "a new type of life" is STILL too "from-something", let's go back to Day 3 when G-d created plant life from a Word. Clearly, that is ברא, and this tomato is simply an echo of that act of Creation.
G-d helped that fertilized seed create that tomato life. G-d created tomato life as a species. G-d categorically created plant life from Word. Each of those are ברא, and not יצר (potter crafting a bowl) or עשה (arranging things together).