Tanjamuse provide me an example library where I did some tests. In order to tie up my loose ends in this thread, here is the solution that fits to her needs.
Code:
program:
tmp1 = template('{#fandoms:sublist(0,2,&)}{#fandom_secondary:sublist(0,2,\,)}/{author}/{title} ({#story_id})');
tmp2 = template('Crossovers/{#fandoms:sublist(0,2,&)}{#fandom_secondary:sublist(0,2,&)}/{author}/{title} ({#story_id})');
tmp3 = template('Multiple Crossovers/{author}/{title} ({#story_id})');
cmp(
count(
field('#fandoms'),
','),
2,
re(re(tmp1,': ','_'),',',' - '),
re(re(tmp2,': ','_'),',',' - '),
tmp3)