Trying to look ahead, it seems that writers might need to ultimately build a publishing brand, as opposed to a mere author brand. That would alleviate some of these pen name/genre problems that become apparent when you have a number of books out.
It also opens the door to the rather alluring idea of eventually publishing other authors as well. Not to mention more complicated tax issues. Is this where indie writing is headed, ultimately? Indie publishing houses could serve as, ha, gatekeepers, insuring a known level of quality.
It's apparent that traditional publishing companies are going to get more aggressive toward the ebook market, as evidenced by recent price cuts. We may soon be facing a day when your book is put head-to-head with publishers instead of individual titles. Having an identifiable publishing brand might soften that a little bit.
I know the argument that readers don't buy from publishers, they buy authors and stories. But they recognize publishers, nevertheless. It's likely that having a publishing company, any publishing company, will help indie writers in the long run. A hedge against changing markets, if you will.