Right now, zync is managing routes for every service. When the public base URL of service is updated, zync updates hostnames of routes in openshift. This is a problem for custom apicast.
Example:

1. Create and configure service in 3scale (Zync creates routes in openshift for default URLs for staging and production)
2. Deploy custom apicast inside the same project as 3scale or in another project
3. Create route for your custom apicast (e.g. my.apicast.example.com)
4. Change public base URL of staging/production in 3scale admin portal to new hostname created in step 3 (my.apicast.example.com). We want to redirect traffic to custom apicast.
5. Zync updates default routes (created by zync in step 1) of service to the new hostname which disables the route created in step 3 because openshift will choose older route when 2 routes have the same hostname
   That means hostname (my.apicast.example.com) is still connected to apicast-staging/apicast-production but not to custom apicast.

There exist a workaround, when you change target service of openshift route (instead of apicast-staging/apicast-production you target it to your custom apicast). But this workaround works only when the custom apicast is deployed in the same project as 3scale.

I would suggest that the service should have the option to disable creating routes, which means that we can create service without routes on openshift. This would solve problems connected with custom apicast.

See linked issue THREESCALE-3001.