WOO THEORY TIME!
If I'm not mistaken, Mugetsu isn't what caused Ichigo to actually lose his powers. He would've lost them anyway, it was just a powerful attack that probably spread up his time limit (before his powers ACTUALLY started going away).
And I don't think your reason makes perfect sense either. Because of his new form, his reiatsu is not recognisable by his body, and so he can't use it?
I like comparing reiatsu and reiryoku to a light bulb and a battery, respectively. The light from the battery (and therefore the reiatsu) is always visible, even if the amount of light can be increased/decreased. If the lightbulb were to change into a buzzer, let's say, you could still hear the noise that is made (the reiatsu would still be there) even if it is of a different type.
Unless I'm cpmpletely misunderstanding?