OK i'm a real FNG at d20 and starfinder is my first game like this. I come from tge dark heresy rpg by FFG, gurps and other game systems.
So i'm working on TRON 2087, an android engineer and I thought of taking skill synery as a first feat but was told it was a waste as at a couple levels my bypass would override my insight bonus to mechanics and computers.
OK but what if I took skill synergy and aplkied it to physical science and perception? Those don't get an insight bonus from bypass so I would basically keep my 2 bonus to them as my level rose, right?
My exocortex gives me a skill focus I can put at like engineering or computers for a +3 until my bypass equals it then I could switch my exocortex skill focus to another skill that my bypass doesn't boost, right?
I am slowly learning the system. I'm used to more simulationist systems but am getting it. I would like my first character not to be a trainwreck because i'm unfamiliar with the system.
Yes, if you don't plan to apply anything else with an insight bonus to physical science or perception then skill synergy would work with those. Perception is definitely a good skill to get that bonus on, but note there's a mechanic trick, Visual Data Processor, that can apply your bypass insight bonus (which scales from 1-6 as you level) to perception if you choose to go that route.
Just my personal experience as an eco mechanic: I'd question the value of going this route. Perception is great and all, but wisdom isn't likely to be a strong stat for you which is going to be limiting. As for physical sciences, it's really one of those "it depends" skills. In some adventures it might come up a lot, in others not at all.
I'm not saying it's a horrible choice and as you said the things you'd really want to boost are already covered another way. And other choices you make (e.g. visual data processor) might factor into that choice.