Here is a breakdown of my setup, starting from the production side:
Basically it's a huge bot base. All fruits are produced on-demand (tower only enabled when there is logistic network request for the corresponding fruit). I overplanted everything so there is always a ripe tree when I need its fruit. The harvested fruits are immediately air-lifted (by bot) to a bioflux maker block, and processed in their freshest state (99.5% fresh):
The upper block here makes the bioflux. It only starts requesting fruits when there is orbital demand for science or bioflux. Fruit crushers are throttled to avoid overstocking the easily-rotten mash / jelly.
The science block requests bioflux (99.0% fresh) and eggs over bots. Since eggs rot quite fast, the requested eggs are laundered with one last round of reproduction and direct-inserted into the science maker at 100% freshness. On the right side is an egg brewer, which slowly cycles eggs in a normal biochamber normally, mass-produce eggs when there's demand, and burn eggs to a manageable level when demand is gone. The sciences are belted to rocket silos, and launched at 98% freshness.
All the blocks use fish for nutrients.
Next comes the transport part. With legendary thrusters flying speed is never an issue, the real challenge is to avoid stockpiling science on Nauvis, or worse, on space platforms. This is what naturally happens when one just requests for science on the Nauvis hub and space platforms.
To this end I built an iron-stick ticketing system:
Basically, I have a fleet of identical shuttles. Each shuttle loads 14k science on Gleba, while making 1 iron stick during the trip. The Nauvis hub requests 3 iron sticks, representing a stockpile of 3*14k batches. Each shuttle only leaves Nauvis when its iron stick is gone. The hub also makes a really large science request to ensure all shuttles fully unload. and destroys iron sticks as science gets used up.
This way, the shuttles maintain a staggered schedule and never stockpile science themselves. Every science gets transported to Nauvis fast and hopefully gets used before it rots.
After arriving at the Nauvis hub, the science just gets air-lifted again by bots to each lab. This sounds stupid and uses a lot of power, but it's actually the fastest method with enough worker robot speed research.