Normally I talk about overlays in the context of data center/SDN/cloud but today I'm going out into left field and am going to talk about voice! :-)
I freely admit that I'm a noob when it comes to Cisco voice so I'm not sure if the behavior I'm about to describe is obvious or not. It wasn't obvious to me and I only figured it out after running into the issue for real and troubleshooting it to resolution.
The issue stems from my misunderstanding about how dual-line ephone-dns function when used in an overlay.