Does the customer pay for shipping twice?

No. The split happens after checkout, so what the customer paid doesn't change.

What if the pre-order is the only item in the order?

Then there's nothing to separate, and the order stays as it is.

Can I separate pre-orders and also respect a carrier weight limit?

Yes. The pre-order rule runs first; a shipment weight or item limit is then applied to each resulting shipment.

How to ship pre-order items separately on Shopify

When a customer buys an in-stock item and a pre-order in the same order, the in-stock item shouldn't sit on a shelf for weeks waiting for the pre-order to arrive.

Short answer: If you sell pre-orders through Shopify's own pre-order purchase option and split shipping is active in your store, Shopify already puts them in a separate shipment at checkout. If your pre-orders are marked with a tag or a collection — or come in as draft orders — they land in the same fulfillment as everything else, and you split them by hand or automatically with a rule.

Watch: one rule ships pre-order items separately (36 seconds).

Option 1: check Shopify's split shipping

Shopify's checkout can split a cart into several shipments when items can't ship together — pre-orders made with Shopify's pre-order purchase option are one of those cases. Look under Settings → Shipping and delivery; in stores using shipping options by market it's always on. The customer then picks a shipping option for each shipment.

Option 2: split one order by hand

In your Shopify admin, go to Orders and open the order.
In the Unfulfilled section, open the ⋯ menu and click Split fulfillment.
Choose the items (and quantities) that should go into the new fulfillment, then click Split fulfillment.

This works on the desktop admin or Shopify on the web, not in the Shopify mobile app. If you split by mistake, the same menu has Merge fulfillment to put items from the same location back together.

Option 3: separate pre-orders automatically with a rule

Install SplitFlow from the Shopify App Store.
Create a rule of type Separate matching items.
Set the condition to Product tag equals pre-order — or Collection equals your pre-order collection. Add a second condition with AND to narrow it to one launch, for example a tag and a collection together.
Click Preview latest order to check it, then save.

Pre-order items now move into their own fulfillment order, usually within a minute of the order arriving, and the rest of the order can ship straight away. It works for online-store orders and draft orders alike. If you want the pre-order part to wait until stock arrives, put that fulfillment on hold from the order page, or with a Shopify Flow workflow on the Fulfillment order split trigger.

Questions

Does the customer pay for shipping twice?: No. The split happens after checkout, so what the customer paid doesn't change.
What if the pre-order is the only item in the order?: Then there's nothing to separate, and the order stays as it is.
Can I separate pre-orders and also respect a carrier weight limit?: Yes. The pre-order rule runs first; a shipment weight or item limit is then applied to each resulting shipment.