What happens for "NDC tickets" is that there is a published fare and then there can be either discounts or surcharges in the tune of 0-20 EUR compared to the published fare for European flights at least. Lufthansa does the same for sure. This means that a Z ticket with 15 EUR surcharge would cost 5 EUR more than an O ticket with 0 surcharge, it is quite a mess since O is a higher booking class than Z. If you want to book at published fares, it goes via GDS... but AY will add a 15 EUR per direction YR/YQ distribution fee (on top of the fees charged by the travel agent), which means that in most cases, for European flights at least, the published fare + YR/YQ fee should be equal or lower than the NDC price for direct sales.

Note that "finnair for business" fares at the moment seems to be based on the published flex fares only. In the past it was also a way to book light or classic, without any discount, but at published fares, without added YR/YQ distribution fee, and without the possible NDC "price surcharge modulation". This means a "finnair for business" flex fare can now cost less than a classic fare, when the classic fare is surcharged by NDC and the fare is not super cheap.

A more honest practice would be to only have discounts on published fares, by booking direct, it is not normal to charge more than the published fare for booking direct.

When doing changes, it looks like quite often the published fares are used, and the difference between fare paid and new published fare is collected. If the published fare is cheaper than the paid fare, they just revalidate the ticket in the same booking class without add/collect if there is no route change.