Yes, it is like 90% rules of thumb and experience. The reason being simulation is expensive: not just in the software itself, but in the time it takes to learn how to use it, set it up for a particular design, and then run through it and understand if it's actually reflecting reality or not. I've been working on some projects where we really care deeply about noise performance, and even the super-expensive packages which exist (which we can't really afford) don't seem to actually be able to answer the questions we have about the design. Autorouting is similar, autoplacing is basically a disaster here.

I am confident a lot of this is an accessibility and UI issue: if you want to disrupt this you could focus on making simulation and auto-placement tools that are cheap and actually usable, and help inform the rules-of-thumb. But that's a very big investment and mostly orthogonal to making a different way to specify your netlist.