What is the current best-practice/preferred method with metromaps and dark/light modes? Is it to just use an opaque light-grey/white background and produce a single metromap such that the image is always consistent?

I always make two, depending how you make you it and in which software - I use Ink scale - You can just type select (text) or maybe colour select 'all of them same' and then change the Hex to white or black depending which mode I started with. The light grey method is also valid

I downloaded inkscape because my usual design tool has dreadful SVG import behaviour. I am also rapidly realising that my pipeline is a chaotic spaghetti of tools and inputs which don’t all proceed in a nice linear manner and I am currently doodling possible layouts on paper because its faster haha

excalidraw is a nice middle ground between a formal metromap and hand drawn process maps.

I had the same with #viralmetagenome, here deciding which tools/steps were important enough to make the map helped. I simplified the overall pipeline a bit to make it more accesible

Simplifying is definitely completely valid. These types of diagram are not meant to be technical but aimed at overview understanding (and also why im frustrated we cannot already test Metro flow... I'm still rather skeptical)