Yes, reading filters are different than custom access groups -- your custom friend groups on LJ will be imported as custom access groups, not custom reading filters.
(Well, they will once we finish up the bits of the importer having to do with friends. Right now, if a post was locked to a custom friend group, it gets imported as still being locked to that custom access group, and the custom access group is created, it's just not populated with anyone, making the post effectively private. At the moment, you have to manually repopulate it. We still haven't made the last set of decisions about how we're going to handle that -- whether we'll populate them with OpenID accounts for your friends from the service you're importing from, or leave it blank and let you re-create them with those accounts on DW.)
Re: Filters
(Well, they will once we finish up the bits of the importer having to do with friends. Right now, if a post was locked to a custom friend group, it gets imported as still being locked to that custom access group, and the custom access group is created, it's just not populated with anyone, making the post effectively private. At the moment, you have to manually repopulate it. We still haven't made the last set of decisions about how we're going to handle that -- whether we'll populate them with OpenID accounts for your friends from the service you're importing from, or leave it blank and let you re-create them with those accounts on DW.)