We really have two issues we'd like to solve. If we solve #1, we don't need to worry about #2. Just discovered Script Editor, hoping it can help. We're on the Shopify Plus plan.
1. If a customer goes to checkout with Product A (which ships right away) and Product B (which has a dispatch date in 3 weeks), we'd like the checkout page to show:
a. Ship items together in 3 weeks - $1
b. Ship items separately when each is ready - $2
2. If we cannot do #1, then can we include a message on the cart page, near the checkout button, that only displays when the cart contains both Product A and Product B. "Shipping price shown will be for separate shipping. If you want to ship your items together, we will refund one shipping charge" or something like that.
This can be done by including those Shipping methods in all shipping regions in your store then having a Shipping script delete those special methods if Product A and B aren't both present. I've got experience working with Shipping scripts to do just this type of thing and would be willing to discuss helping out if you are still in need of this functionality.