The way I understand it is that they are subtly different by design (and I am certainly open for correction): filter(A, B) will first filter according to A and then subfilter according to B, while filter(A).filter(B) will return a row that matches A 'and' a potentially different row that matches B.

Look at the example here:

https://docs.djangoproject.com/en/dev/topics/db/queries/#spanning-multi-valued-relationships

particularly:

Everything inside a single filter() call is applied simultaneously to filter out items matching all those requirements. Successive filter() calls further restrict the set of objects

...

In this second example (filter(A).filter(B)), the first filter restricted the queryset to (A). The second filter restricted the set of blogs further to those that are also (B). The entries select by the second filter may or may not be the same as the entries in the first filter.`