Sure I'll take a swing (and am an XP producer):

How do you make factories, and therefore XP more communal without making prot and tools more expensive?

Prot and tools should be more expensive... However, if you wanted to not make them more expensive, you could make gigantic batch sizes which would go part of the way there.

Should XP be "throw all items in and get XP," or tiered like Bastion factories?

Not just for its own sake -- tech trees don't make sense in a game like this, because unlike a RTS that starts over constantly and only has enough time to follow one or two branches of the tree (thus strategy), civcrafters just build all the branches (thus no strategy, only more clicking).

However, a little bit of tiering would help to allow larger batch sizes for some things (by filling up whole double chests and then the results going into a second recipe), see point above

Do we need multiple recipes?

I'd say NO, actually. Just one with more variety than currently. Multiple recipes only accomplish less cooperation, by allowing more diverse places to have everything they need at once. One big complicated recipe forces a variety of biomes to be involved. Ideally, all biomes for diamond cauldron.

Ask yourself: what would force you to share your factories? A bastion factory-like radius? Doubling repair costs? Revamping repairing?

• Not having the physical land resources required due to high recipe variety of ingredients. Somebody's idea below about "quality" (lore perhaps) of ingredients to get around the fact that biomes aren't exclusive enough could work very well.

• Not being able to bot as well as anybody else can bot an ingredient without a ton of effort -- I can think of no way to accomplish this though.

• Repair cost could do it but would have to be a hell of a lot more than doubled. For many factories, even if it cost as much as a new factory, it wouldn't even be enough. I could build a new bakery or stone smelter each month by myself no problem and still have it be worth it.

Why do even the most trusted friends forgo starting a business and instead producing alone?

Organization is work, and setting up enough bots and such to be equally as efficient as anybody else in each ingredient is not difficult enough to bother.

The map is going to be sharded. How can an XP rebalance make sharding more meaningful?

ttk very clearly didn't want shard to be impediments to movement, thus I don't think it can really contribute much.