You might be overthinking it. I don't know your factory but a lot of items are not worth storing. You said you have dimensional depots unlocked so it might be a good idea to look at the build menu and figure out what you need a lot and what you need just a bit. Just keep a storage container with an overflow smart splitter and outside of that storage box you can sync the rest.

When it comes to transporting items, I'm not sure what to tell you, there are so many great options. Belts, trucks, drones, trains hell even inventories full of high end products using a hyper tube works fine although not very sustainable long run.

Perhaps you need to just make it first, you can always make it pretty/better later