> The refactoring bit hits hard, how do you structure your factory to minimise time/cost/space, can you increase throughput, do the outputs line up where you need them, how do you ensure a sufficient power supply, etc.?

There are different 'designs'. I'd recommend a main bus design for your starter base. Basically you take key materials, like copper plates, iron plates, steel etc. and then run (multiple) full belts of them down a long line. and build your factories to the side of it, taking your input materials from the main bus.

See here: https://wiki.factorio.com/Tutorial:Main_bus

Alternative designs (for much later in the game, if you want to buiold a megabase) are e.g. rail grid, sometimes called city block design. Looks like this: https://i.ytimg.com/vi/1as3oMAgOy4/maxresdefault.jpg

You have a grid of rail tracks with standardized squares and standardized input/output locations. Then you automate input delivery/output collection to them either by pure circuit logic, or of you don't hate yourself quite that much using the Logistic Train Network mod: https://mods.factorio.com/mods/Optera/LogisticTrainNetwork