Again, nothing specific to bundles there. The issue with Scrivener is that it updates its files so often that *any* online storage system will struggle to upload the files fast enough to keep them in sync. That's not a problem with bundles, it's how that particular program deals with files.
Again, bundles aren't special - they're just folders. Want proof? Make a folder, give it a name with a .app suffix. The system will suddenly think it's an application! Of course, you can't launch it because it's just a folder.
A counterpoint to your argument are programs like 1Password. They use bundles, just like Scrivener. However, because 1Password was written in a better way than Scrivener, it works just fine with Dropbox - in fact, Dropbox is the reccommended way to keep 1Password in sync.
So, to sum up. There is nothing inherintly special about bundles that makes them problematic with online services. Saying that is silly, as they're literally just folders. The problem lies with specific applications and how they deal with files. In fact, applications with large monolithic files are much, much worse with services like Dropbox as the entire file needs to be re-uploaded when the tiniest thing changes.