nope, the part in functions.php just caches the content of templates, that you don't have to catch em from the db with every call.
you always have to define variables before you can use them.
example:
PHP Code:
eval("\$cust_header = \"".gettemplate('cust_header')."\";");
eval("dooutput(\"".gettemplate('cust_main')."\");");
now you can use $cust_header in your cust_main template