So am I correct in assuming that ABE rules apply to whitelisted(or temporarily allowed) sites ONLY? Meaning that using ABE rules I can specify more precisely on which sites a given domain in the whitelist can really be used and for which it will be denied DESPITE being in the whitelist?
The short answer is "no".
An extract from that very section 8.10 of the NoScript FAQ:
Notice that since ABE's rule work independently from NoScript's permissions [...]