It is kind of troublesome since abilities go on cooldown after "Starts the effect of an ability". And that triggers after the time specified in Art - Cast Point has passed. The time starts when a unit "Begins casting an ability". Most units have 0.3-0.5 seconds cast point time.
I'm thinking you'd have to use custom casting system. Set cast point to 0 and use last order library. When you just want to set an ability to cooldown, order the unit to cast it, then after a 0.00 timer, order some past order using the library, so it looks like the unit never used the spell. That will reset animations though.
When you want to really cast the ability, you could give the unit hidden dummy ability based on channel, which then has the channel/follow through etc times you want.