I guess the easy answer is "No, you can't. Live with it." :)
The hard answer is that Tridion already has a rather powerful (and complex) conflict resolving algorithm that takes blueprinting into account, and adding the possibility of merging different blueprint trees - which is pretty much what you're asking for - would make that complex logic a lot more complex by a few orders of magnitude.
When you read an object in CM, Tridion navigates "up" the Blueprint Tree to find the actual object's content and properties, and having multiple branches that contribute to the current publication without a common parent just explodes the number of possibilities. The correct solution for what you want to do is typically addressed in the BluePrint design by:
- Following the Diamond pattern
- Always - and I mean always - have an empty publication as your Blueprint Root.
In other words, we could make this possible if we thought it would be important enough. But frankly, we don't think the benefits of being able to do this outweighs the cost of creating and then maintaining a very complex resolving algorithm (with most of its implementation in the database layer).