Therefore my question: Is local.cf the last ruleset to be processed by SpamAssassin? In that case I can take the modified scores to local.cf.
No it's not the last file parsed, user_prefs is. AFAIK processing order is:
/usr/share/spamassassin/*.cf (processed in alphabetical order) /etc/mail/spamassassin/*.cf (processed in alphabetical order) ~/.spamassassin/user_prefs
Note: depending on compile options and your directory structure the paths may be different than defaults (ie: /usr/local/share.. etc). However, the general theme of default rules in alpha order, site rules in alpha order, and lastly user_prefs still applies.
So, you can either use user_prefs, or a file in /etc/mail/spamassassin which comes alphabetically after all your SARE rules. Local.cf might work depending on which files you use, but zz_sare_scores.cf will certainly run after them.
