Fortunately there is (finally!) an open source PCB design program that doesn't suck: Horizon EDA. I've only made one PCB with it but honestly it was pretty great and the author fixed every usability bug I reported in a matter of hours, which is an insane difference from KiCad's "you're holding it wrong".
The only think I don't like about it is it has an unnecessarily powerful and confusing component system (there are modules, entities, gates, etc.). But really it is the best by far.
Anyway, on FPGAs, I think the tools are only vaguely mature for iCE40 and even then you basically need to already be an expert unfortunately.
I've only recently starting designing PCBs and I started with KiCad, but I've found it to be very easy to use after watching one video of someone going through a simple board design.
I didn't need a video to figure out how to use Horizon.
I have yet to design a PCB where I didn't have to create basically all of the components myself.
I am curious to know if you are using Qemu by any chance to prototype your hardware. I am doing some work on Qemu to make prototyping easier of a custom hardware and would love the pain points.