You're gonna need to expound on --deep being broken, considering I've not run into a single issue with it, and judging by the majority of blog posts/docs that cover this, others have the same experience.
I'm assuming it doesn't work well with nested bundle signing. As per my other thread it also seems to be picky about which subdirectories it signs, and there are lots of weird paths (LaunchDaemons, XPCServices, LoginItems, etc) you can put stuff in that needs signed. Not to mention if you put anything needing a sig in Resources.
Hmmm, well I'm willing to believe it then, yeah (although I definitely have a nested bundle setup in a project where --deep works fine... odd).
This is good to know though, and hopefully this exchange helps someone in the future too (actually, this would make for a good blog post - this kind of nuance is lost in most of the docs/existing posts).