Fair point! Fruits are meant to be eaten, though we rob the plant of its purpose by defecating in toilets instead of spreading seeds around, or simply removing the seeds before eating.
PS: Though going another extreme, some would argue - what about the microbiome that exists within the fruit?
The microbiome of the fruit would join with that of your gut unless you cook it. Surely some type of microbes will be killed in your gut but at this point I think we swing back around to synthetics if you're worried about that.
Because we can't avoid causing pain 100% doesn't mean we should stop trying avoiding causing pain. That's the mentality behind ahimsa diets.
We can avoid most pain with synthetic food. It could also be higher quality, taste better and be healthier for humans than plants and vegetables. There's been a lot of progress in that field in this decade. Still a ways off though.
I'm not sure there's such a thing as synthetic calories and I'm not sure this is possible. Lab grown meat is another thing. It is very much alive.
Definitely exists. They are commercially available already in primitive forms, such as Soylent.
As for meat, you mention cultured meat, that is lab grown. While you're right that it's alive, it's a massive step forward as it's not connected to a nervous system.
But there's also purely synthetic meat - there's been a lot of development in this field. It's still a few years off, but they'll get there.