I wonder if the OP is referring to the following:

Sometimes AC will create an "add-on" fare for outstations that can be added to a published fare. So for instance when I recently bought a good P fare from YOW to JNB/CPT, it was actually priced as YMQ-JNB/CPT with a YOW-YMQ either $50 or $100 add-on (I forget which one), called I believe a "constructed fare". An interesting thing is that one does not actually need to go to YUL (YMQ) to use it, so I am flying YOW-FRA-JNB not YOW-YUL-FRA-JNB; and could have taken YOW-YYZ-... if I preferred.

In that case, it is possible that the YGK-YTO add on is defined for YYZ-LHR fares and so OP can fly YGK-YYZ-LHR for just $100 more than YYZ-LHR. But that AC has failed to allow a YGK-YTO add-on for all?/some? transborder fares, and therefore OP is obliged to buy a much more expensive YGK-YYZ and YYZ-US fare combination.

I have myself flown out of YGK rather than YOW on occasion to international and major US destinations and had no problem, but haven't tried to smaller points.

If this is indeed the issue, then AC's reply is technically correct in that it is not an error, it is that someone at AC just didn't find it important enough to create a constructed fare for that specific city pair. It is also doubtless quite annoying, since it's not the result of a strategic decision to not "be competitive" on this route/market, but probably just not finding it important enough to bother.