Why are alert/confirm dialogs bad for mobile web?

I'm currently working on a mobile web app with external designers, but we (the developers) are allowed some input. They keep wanting to add alert and confirmation dialogs for things like form validation, signing out, deleting things, etc, which raises UX red flags for me - they just seem wrong on mobile web apps for some reason and I can't pinpoint exactly why.

Worse, they keep asking for things that alert() and confirm() can't do, like using "Delete/Cancel" or "Yes/No" instead of the default "OK/Cancel", or disabling the "Prevent this webpage from creating additional dialog" checkbox that appears on modern browsers. The only way to do this, of course, is to create custom dialogs, which raises even more red flags.

Is there any research or authoritative articles on why this is bad? Or am I just going crazy?