You can vary content using one script, call it index.pl, which is in your private /cgi directory. It can run as the index of both foo.com and foo.com/members by placing the line DirectoryIndex /cgi/index.pl in .htaccess of each directory. If your index.pl prints from a template, use a relative path naming index.tmpl and the script will pick up the template which is in the directory it is called from.

When in the members area, (assuming you have used one of httpd's auth methods) you will have $ENV{'REMOTE_USER'} defined, which can be used for conditional execution or output.

There is no reason you can't conditionally execute (system, open, etc.) or include (do, require) external programs, but it may not be as necessary as you think.