Am I making too much of a big deal about this? Is it simpler than it seems in my head?
Yes, this is indeed the case. Once you have set up the front suspension to your liking, I bet that you will never touch it again. Having a pillion on, or off, the bike, makes no difference to how the front performs. At the back, flicking the lever to hard or soft is all that is required. In fact, I don't even bother with that, I leave it on hard permanently because that gives the bike more ground clearance for cornering.
Now, I am going to stick my neck out here. There is a myth about suspension that not even Yamaha understands. And that is that adjusting the preload makes the suspension harder or softer. It does not. All preload does, is adjust the amount of sag in the suspension. Thus, if you screw the preload adjustment down by half an inch, the suspension will extend by half an inch, and that is all that happens. You now have an extra half an inch of suspension travel available for when you hit a bump, but all else remains the same.
The only way that preload adjustment could possibly make the suspension harder, is if the suspension reached the full extent of it's travel (tops out), and you continued to increase the preload, then the suspension would become harder. But, this is not possible because the preload adjuster does not have enough travel to do that.
As for damping adjustments, the Gen 3, A model, only has adjustment on the right hand front leg. Rebound adjustment is by a hand operated clicker at the top of the leg, and compression adjustment is by a screw driver operated clicker at the bottom of the leg. The rear shock has a hand operated clicker for rebound damping only, positioned at the bottom of the unit.