Can i file 2 different tax returns (self employed vs rental property) for me and my spouse and pay the 2 different fees or do i have to file them separately?

 If you are preparing your return together with your spouse, then you will be using the same version of TurboTax and both returns will be charged the same price.

If you want to use a different version than what your spouse is using, you would have to prepare your returns separately.