The "penalty" is going to depend on what they think your reason for doing this is[1]

They can easily look up all historical prices.

I once sat in an AC corporate office where I was told (with no guarantee or assurances) that I'd be fine to skip my first segment on an upcoming trip[2].

But it was also made very clear to me that if YYZ-TYO is $1000, NYC-YYZ-TYO is $500, and you try it, you're asking for trouble. Whereas if NYC-YYZ-TYO is $1200, they might not view it as you trying to breach the tariff to save money.

[1] And whether they catch you, and whether they have the resources at the time, etc., but your ACTUAL reason is irrelevant
[2] I ended up paying a change fee because I didn't want to play games