From my limited personal experience (I can cite about 3 occasions in the past 12 months, both on AA.com and by phone, where a ticket that violates a 'rule' has been issued nonetheless), the pattern seems to be where application of the rule would result in a prohibition of AA-metal flights.

For example, HA's rule for SYD-LAX permits SYD-HA-HNL-AA-LAX. But XXX-SYD-HA-HNL-AA-LAX is prohibited (forget about the VA requirement, I'm talking HNL-AA-LAX).

I postulate that AA isn't keen on forcing people OFF AA metal and ONTO HA metal, so it seems that AA's fare rule is used in this case (there is an AA fare rule which permits XXX-SYD-HA-HNL-AA-LAX).

If this is so (which is speculation based on reverse-engineering), I'd doubt it is done on a per-citypair basis, but probably more generally (e.g. "Zone 1 to Zone 3 where TPAC is on HA, AA fare rules used").