> There wouldn't be any wasted energy due to the inefficiency of photosynthesis...

Honestly, tomatoes are really efficient as is. They grow huge amounts of fruit per acre; they grow in preposterous conditions, like people's windowsills, greenhouses, fields across the world, etc. I don't mean to pick on your particular choice of example, but you really got to get into the weeds to really understand the efficiencies of agriculture.

Indeed, there's consensus that the greatest threat to agricultural efficiency are all the weaknesses of a highly-engineered monoculture. Imagine the devastation of the Florida orange harvest a few years ago due to frost, but due to a single weed.

> a cell is basically a huge finite state machine

There is a huge amount of research to create an "algebra" of synthetic biology, which is really fascinating stuff. You'd love it! You're right that a lot of what you're describing is inevitable, but there's a huge grind to get there, solving engineering problems totally orthogonal to the theoretical biology of it all.