While I see your point to a degree, I’m wondering why you think you can’t edit the PHP files required to modify those aspects of a theme that you want to change?
WordPress provides you that ability from within the Admin back end, with the “theme editor”. For example, removing the hardcoded “links” from the Diary Notes theme’s sidebar (those are not “Blogroll” links - you can edit the “blogroll” separately) takes about two minutes to do (if you are slow!). All you have to do is edit the sidebar.php file using the theme editor, remove (or change) the links, and save it.
That said, I’d rather have DreamHost provide the widest variety of themes for us to tweak, as we can’t add new themes to the “easy” one-click installed WordPress instances. I also understand and appreciate them not overly modifying such themes “pre-installation” (other than their own blogroll items, which you can easily change) as these “free” themes were provided by authors at no charge. It is reasonable that their initial work be delivered as they intended. I think this is appropriate even to the extent of linking to a “sponsor”, “favorite sites”, or “friends”. Sure there are some link-abusive “free” themes out there (hidden links, too many links, etc.), but I have not seen any of those in the DreamHost package.
If you need help modifying a particular theme, there is always someone here that is likely to be able to help you, and there are certainly many such folks on the WordPress support forums.