I'm guessing that Sage is designed on the philosophy that if you've got to ship an order in two parts it's going to cost twice the carriage as sending it all in one go and so it's making the customer pay for your lack of foresight in not having enough stock, as opposed to you having to absorb the extra carriage cost (as a useful reminder to ensure you have the required stock in future)...

...Or it could be that nobody at Sage actually thought about how part shipping would/should affect carriage charges, and it just blindly adds the full amount to each invoice.

With regard to how to ensure you absorb the extra cost, I've no idea (if there is no way it may be worth adding a suggestion), but when I was working in mail order retail¹ <mumble><mumble> years ago² we had stock codes (there were more than one method used with different prices) for delivery³ - not the best solution but it did allow part shipments without full delivery costs on each [part] invoice. 

The system actually created a pick list based on the outstanding order and once picked the invoice for shipping was created based on the pick - a part order being shipped resulted in an invoice for that part, along with any carriage charges for that part [if any left].  (For reporting on shipped orders, writing it in Pick Basic to access the database was very easy to skip the carriage charges if necessary.)

¹I'm now working in a service industry with no physical goods to ship, and have only used Sage in my current job on a desktop PC.  When working in mail order retail I was the computer department looking after a Honeywell DPS-6 mini running the mail order system and accounts - that system is my benchmark for ease of use.

²some time last century - things should be much easier now considering the computing power on the desktop handling one user, along with the computing power of a server for the data, compared with the central mini handling around 110 users (accessed using "intelligent" terminals) and around 10 printers.

³with a ridiculous amount of stock, zero cost price, and a handsome profit with the sale price over the actual cost of shipping⁴; I hate to say (admit) it but carriage was one of the most profitable items that was "sold".)

⁴the actual cost depended upon a few factors at actual time of shipping, but unlike British Leyland and the mini, they did know the costs and so shipping was priced to be more than this to provide a profit.