The situation you describe would certainly affect the tuning of the speakers' bass - and the influence would probably be heard up to (I'm guessing) 600Hz or more.
Preferable, if possible, would be not to enclose the speakers at all, but hang them from the upper surface, further outboard of where you have them pictured, and angled in a little bit while you are at it. If you use a single (long) screw from the outside of the cabinet into the center of the speaker top, you could play with the toe in angle as well!
You might also consider a small piece of black foam just above the tweeter to help kill the first reflection off the top of the cabinet.