How is the excerpt retrieved?

Hi folks,

I have inside the excerpts shortcuts from other plugins (RB Internal Links) which were not evaluated when the excerpts are shown.

I changed in /atahualpa/funtion.php the return values of all exit branches from bfa_wp_trim_excerpt($text) to do_shortcode($text) - but it didn't work.
Then I had a look at ATO option "style & edit Center column/The loop" since I assumed that there would be specified, how Atahualpa overrides the default loop behaviour.
Only after changing the function the_excerpt() in /wp-include/post-template.php the shortcodes were evaluated correctly.

I'am new to WP 3.0 and Atahualpa 3.6.4 - here are my questions:

(1) how and where is bfa_wp_trim_excerpt($text) called?
(2) why didn't worked the changes in bfa_wp_trim_excerpt($text)?
(3) what is the ATO option "style & edit Center column/The loop" for?

Thnx
Michael