Each store has it's own checks and balances. Now would it be cool if what you bought on one would send a signal to the other and allow you to download it? That would be nice but whats the point?
Android is hackable and open. After a few days Fire TV will be rooted and the playstore will be loaded. Once that is done then your free to install everything from both.
Just as you said that one place was on sale and one wasn't that is what I love. You have a greater chance of finding stuff on sale!