Are there disadvantages to using different Apple IDs for iCloud and Store purchases?

Apple provides instructions for configuring one Apple ID for iCloud and a different Apple ID for Store purchases. But this is clearly not the "recommended" approach.

Is there a reason to avoid doing this? Are there disadvantages, such as lost integration, or omitted features that result from using different IDs for iCloud and Store purchases?

As of right now, there are no disadvantages. In fact, my fiancée and I do this right now. We share an AppleID for store purchases and set up Home Sharing so that our iPads and MacBooks can share apps, but we have separate iClouds on our machines and everything works fine.