In my view, the "slot method" is meant to be used when there are no repeating items. It's not meant to be a catch-all approach for every permutations question.

It works fine for most simple permutations questions because most simple questions don't have repeated elements. Luckily, this covers most GMAT permutations questions.

The slot method cannot work for situations when there are repeated elements, because it cannot take into account things like: "Was the thing I put in the first slot one of the repeated elements, or was it not?" It is designed to be used for situations in which there is no uncertainty about any given element's availability for future slots.