Yeah, you can do that -- just hit the Ship button for one, adjust the weight for both, then mark the other as shipped in eBay. I do that all the time.
As I understand it, though, the only problem is that PayPal won't help you out if you have a dispute. I think that's because they want to see Delivery Confirmation for each invoice. What some people do, I think, is to refund the two separate invoices through PayPal and send them a new combined invoice -- just to satisfy PayPal in the event of a lost package or whatever.
That seems to me like something that might annoy some customers, though, so I usually just do what you described above.