I’m actually the editor who added the K-ON series.
I honestly don’t know if there is any standardization on how to slice up a series. someone else had already added a couple series for the K-ON character songs, so I added those as subseries. then I just threw the rest of the release groups into a single series, since that made sense to me at the time. granted, K-ON seems a bit of a simpler case than Maitetsu, since there’s only two anime seasons, a movie, and some audio dramas. (technically also a couple manga, but those don’t usually have audio content 
)
I’d probably slice up release groups in the first 2 ways you listed, depending on how connected the release groups are.
for example, if there’s two anime series that have pretty much the same characters and one just continues the other, (like K-ON! and K-ON!!, depending on how you slice it), I’d probably have the release groups mostly in the same series.
in the case of something like Full Metal Alchemist/Full Metal Alchemist Brotherhood (see Wikipedia), I’d likely do a series for each, maybe with a franchise series linking the two. in this case, there’s some movies a few games too, which I’d add to the series for the franchise as well.
that’s just my thoughts though, there’s not much in the style guidelines or documentation about series to go off of.
(btw, for more discussion on series, see this thread)