The main reason, I suspect, for the TV Series and Season Cover Art to go into a separate folder is that there isn't necessarily a place to put it with the actual Episode media files. There may not be a Series and Season folder associated with the Episodes. Certainly for recorded TV, that is the case. The folder structure is built entirely around the details of the recording, as per the EPG data. Well, for JTV format recordings anyway.
No Series and Season folder structure is enforced when doing TV recordings, but I guess MC could do that, based on rules. But if the EPG doesn't have the Series and Season information, the rules would fail, and then you would have a mess to clean up. But a case could probably be made for moving the TV recording folder setting from "Options/Television" to "Options/File locations", and then adding a rule for the naming of a folder structure, just as with other media. But the rules would need to cope with missing EPG data.
Movie and Audio Cover Art can be next to the media file though. But TV Logos, which are just Cover Art for the channel files, don't have any place to go. Well, not a place you would want people digging around in to add Cover Art.