I agree that this is an apache issue, and the host admin would have to take care of it. But I disagree that this is the default configuration.
I've always been able to have just one ScriptAlias directive and scripts run fine in subdirectories. There is no line like
in the default httpd.conf that came with the 1.3.27 source.
Also, the location of httpd.conf and the position of any ScriptAlias directives are system dependent. Is your Apache installation by any chance from an RPM or other third party package?