Specify all absolute pathnames in Advanced Deployment

Is there a way for all absolute paths to be specified in advanced deployment instead of the (imo) awkward mix of absolute and relative pathnames?

Here is the current issue:
An application that works properly in one Apache virtual host complains that it can’t find the prod runtime in another virtual host.
In both cases, the prod runtime is a subdirectory of the virtual host document root. Their document directories are different.

NB: These are virtual hosts on one physical server (un virtualized) on the same instance of Apache.
Curiously if I try to access the production environment application (eg to configure a datasource) it works perfectly in all virtual hosts.

The setup is necessary to limit what a client previewing or reviewing has access to while a developer (internal or external) has full access.

… alternately, can those pathnames that are set in Advanced Deployment be set at runtime?