I asked this question to support and they suggested the idea be posted here. There are a lot of physical stores that have e-commerce and offer local delivery or in store pick up. Shipstation could be more of a one stop shop, if these kinds of businesses could also use shipstations branded tracking pages for these kinds of orders also.
I could see this working in the following way:
System has two branded tracking pages that can be associated with certain orders.
One that reflects carrier information which is already available.
*IDEA* A second (custom) option, where you can simply click to "Update delivery status", and add bullet points with any notes etc that would appear in the same way that normal shipment updates do in the normal branded tracking page. It would appear like so:
"Order received at certain day and time".
"Product is out for delivery to XXX in store pick up".
"Product has been delivered to XX store for in store pick up".
"Product has been picked up by customer"
Each of these status updates could just be simple text submission by the admin, that would notify the customer when added. This way they could be used for a variety of communication situations.
This would also solve the problem of manual orders not getting a branded tracking page.
Let me know if there is another work around or better idea for this kind of solution.