The linking process for switches is to set the switches to the position you want them to respond on.The full process of linking is to link them at both positions, I simply only linked it at one position.
So I set switch 1 to Off and switch 2 to off and performed the link following Insteon instructions. I did not set both switches to On and link again. This works perfectly for me, when switch 1 is turned off, switch 2 turns off, however, when switch 1 is turned on, switch 2 does nothing. Again, just curious how to accomplish the same in a scene. I'm assuming that EDIT#2 is how I would accomplish the same thing using a Scene? Which makes sense, because that's as far as I got when trying to tackle the new inversely-controlled linking. I'll try it out!
Now the question is, how do I accomplish the new stuff that I'm trying to do, an inverted control. By doing what you proposed in EDIT#2 I can turn off Switch 2 when Switch 1 is turned on, but how do I turn on Switch 2 when Switch 1 is turned off? I can try doing a manual link and see if it works for me, but again, how would I do this in ISY without using a program?