It sounds like you'll lose an input if you get the internal phono stage, but not really...
You'll have to plug the turnatble or external phono stage into something, right? Do you plan on connecting something else, then switching it whenever you want to use the turntable?
Just some food for thought.
The internal phono stage sounds great. I've briefly heard the external phono pre, but not for any length of time. With an external phono stage, even if the board were the same (which they are), there's less noise and grunge. The power supply isn't shared, and other circuitry is further away, lessening the possibility of contaminating the signal.
Keep in mind phono signals are very low, and have to be amplified far more than things like CD players. If there's a little bit of noise, it's far more evident.