You never want to burn fruit itself since that wastes the seeds. So you always want to process fruit the first step.

I limit fruit production based on the number of fruit on the belt, to avoid creating a huge buffer. But after that the factory just runs continuously at the same speed. And if I have too much of a final product, it gets destroyed or burned for heat and electricity.

One benefit, especially in the beginning, is that by processing more fruit you get more seeds. And you need the seeds to expand your fruit production later.

The enemies are probably one of the not ideally designed parts of Gleba. It's trivial to handle them if you know how, and can be very frustrating if you try to approach it the "wrong" way. If you have been to Vulcanus and Fulgora you can trivialize their threat.