Anode Rod Flush?

Pipe threads are tapered to reduce leaks when tight.  That is why normally there will be threads showing on any pipe type connection when tight.

THe only problem you probably will have, is that it will be more difficult to unscrew later.  If possible, I would unscrew the rod, wrap some teflon tape on it, then re-screw it back on.  I use a small socket wrench when screwing the rod back in, but I just use enough force to snug it on...I don't overpower the tightening.  You don't want it so loose that it works itself out...nor so tight that you need an impact wrench to break it loose. 

My anode rod always has some threads exposed after I reinstall it, even when it is fairly tight.
Did you use teflon tape wrapped around the threads?  I always put a couple of wraps of white teflon tape on the rod threads before I reinstall the rod.  The metal on the female part of the rod opening always seems to get a small amount of corrosion. By wrapping teflon tape on the rod, the rod will
more easily screw into the opening.