This perfectly makes sense to me: as soon as you attach an email ER, your code is in charge of handling incoming emails for this doc lib, according to your own business rules.  
So standard settings used by SharePoint when _SharePoint_ does handle emails are not needed anymore in that case.  
Your code will handle email management logic, with dedicated settings you are free to hard-code/store somewhere/etc.

[Note: glad to see you're reusing the code I had posted here http://sharepoint.stackexchange.com/questions/164837/deploy-bind-event-receivers-to-lists-in-single-feature! :)]