I always use eneloop compatible batteries with my Metz 45CT1 in the regular battery basket and never have experienced any problems. When empty, I charge them outside the flash unit with a separate battery charger and then put them back in the basket when full. Works like a charm for me.
Eneloops have a charge voltage of 1.45V specified, which is a little lower than the 1.50V for Alkalines. However, Eneloops (or any NiMh battery for that matter) can usually deliver more current per second than Alkalines.
In practice this results in faster cycle times, and this is where you might want to be a bit careful by not repetitively firing the flash too quickly after the previous flash, as this might heat up the internals of the flash too much.