As far as I can tell, there's two distinct issues:

a) AC is obviously not keen to market connections to an airline such as AA, especially on destinations that AC may also serve or have Star Alliance partners that serve. For instance, SJO, TGU, PTY, etc.

b) Notwithstanding a), if you book a connection to AA, AC will check you in for the AA flights, issue boarding passes onto on-wards AA flights (including printing your AAdvantage number on your AA metal boarding passes for credit to the AAdvantage program), and tag your bags through to the final destination. Even if your AA flights are not on the same ticket as the AC flights.

So what's your issue? Your travel agent/booking websites are unable to, or are unwilling to sell you an itinerary that includes a combination of AC and AA flights? Or are you worried about actual airline 'integration' once you actually fly your itineraries? From my experience travelling on AC and AA, connecting at LAX and MIA, to AA onwards to Central America (SJO, TGU, MGA), there are no issues whatsoever.

AFAIK, an 'interline' agreement between an airline like AC and AA doesn't include any rules around the marketing of flights, in agency for either airline. In such context, it only refers to providing seamless services for passengers who do book and travel on multiple airlines. If your particular vendor-neutral travel agency doesn't offer the ability to select both AA and AC flights as part of an overall itinerary that meets your needs, find a different one, or give their real-life telephone agents a try. Of course, one traditional folly of websites or even dealing with TA's that aren't sophisticated when it comes to fare rules is that you could end up paying a substantially less than optimal fare, especially if it is constructed with a series of individual one-way fares rather than utilizing stopovers, etc., contained in the minutae of fare rules, but not necessarily coded into the websites' search engines.

As for your last question, no, there's nothing route-specific about interline agreements. If you construct an itinerary to any AC destination that is also served by AA, even the smallest and most obscure one possible, you gain all of the benefits of seamless inter-line service. For instance, you could fly YYZ-ALB-IAD, with the latter segment on AA (operated by their regional partner), and expect the benefit of having one-check-in at YYZ, and your bags transferred at ALB.