I've used Paypal to pre-order things, admittedly music CDs and not games, so I wonder if that policy only applies to digital DLs or such? As if so, wouldn't it be possible to set up a pre-order for a physical copy, plus shipping?
Paypal is used for direct transactions. So when you pre-ordered your music CD you probably had to pay for it directly, even though you were going to get it at a later time. Stardock does not charge you immediately after you pre-ordered Rebellion, that's why they cannot use Paypal right now.