The thing is you have no idea if every fare on every route, every day in the identical class is more with the $99 or if yours was an outlier and there are savings to be had on many other routes. You take one circumstance and make a generalization and call Copa scammers.
And you think all airlines with these 2 for 1 or companion fares/vouchers don't lay on the rules to get top dollar for the paid fare so they are not losing money on these deals.
To be fair for your complaint I think some airlines are a little easier to find a net discount like WestJet but then you have to fly a lot to get to their top tier, or have a $400 a year credit card to get the voucher. So they make money overall because 1 or 2% of people actually redeem the coupons. And they have raked in other fees from a larger group.
End of the day, see if it's a better deal or not and proceed accordingly, including checking identical fares.