I wonder if the OP ever found a solution for himself. As far as I know, the only way to work this would be to have all your client accounts on the same server as the scripts you want to include - I've done something similar:
/path_to_myserver_root/httpdocs/clients/client01/wwwroot/scriptA.php
/path_to_myserver_root/httpdocs/clients/client02/wwwroot/scriptA.php
ETC....
THEN:
/path_to_myserver_root/privatefiles/myapp/scriptB.php
wwwroot is where each client domain points.
scriptA.php has some business logic then includes scriptB.php for it's functions with the full path above:
require('/path_to_myserver_root/privatefiles/myapp/scriptB.php')
scriptB.php resides in a private protected dir on the server, inaccessible by http, and not traversable by the clients.
Now mind you, my reasons for doing this is to maintain version consistency across multiple accounts, not to withhold some proprietary magical php code from my clientele - But I suppose it could be implemented for that purpose.
Meh, YMMV.