“Cannot redeclare cpt_reg_tax()” because of functions.php

You cannot use the same function name more than once. Give the second function a different name:

add_action( 'wp_loaded', 'cpt_reg_tax1' );

function cpt_reg_tax1()
{
    // code for the first taxonomy here
}

add_action( 'wp_loaded', 'cpt_reg_tax2' );

function cpt_reg_tax2()
{
    // code for the second taxonomy here
}

Besides that, your code will terrible break for many users, because custom post types and taxonomies are plugin territory.