It has nothing to do with them trying to make money and everything to do with how they're trying to make money. There are a lot of proven ways to monetize your game that have zero impact on the actual gameplay.
By monetizing commanders with unique units and abilities, Relic is letting players pay for more options. If you're trying to compete in a strategy game, having more options is an advantage, so by letting players pay for more options, they're indirectly letting players pay for a strategic advantage in their games.
Now let's pretend Relic implements the CoHO shop system. We have no idea if they will or not, but let's just pretend they do. Suddenly your commanders and bulletins only last a few games before you have to repair them with supply. That's fine and dandy until you realize that your super fancy King Tiger costs more supply to repair than you receive for free after each game. Suddenly you're faced with a decision: do I remove my King Tiger every few games and accept playing with inferior units, or do I pay Relic a few bucks for the privilege of continuing to be able to use this unit in every single game?
If we pretend COH2 will be like COHO, you're wrong in your example.
1- It requires to change the structure of any commander, not much but still into 2 branches.
2- But changing the structure or not isn't important in fact. What make your example wrong is that abilities will always be available for free (as it was in COHO) but Bulletins and special cards dependant of supply.
So your Tiger will always be available in any of your game. But thee +10% vet card you'll use as bulletin will need to be supplied. With probably different level of card bonus (who knows maybe a +10% vet, a +20% vet and a +50% vet) and each of them would have a different cost supply.
if really Relic copy/past COHO system, maybe new "veteran" units will be available. Like a veteran panter tank with better stats than the basic one and here again, calling this veteran unit will cost you supply, but here again nothing would stop you to use the basic unit instead.
And for tournament, you can easily control the usage of such units/bulletins. You can prohibit supplied items from your tournament. Or you can as well impose a limit of supply for each game or per phase. Pool phase = XX amount of supply, 2nd phase = YY amount etc... putting a bit of macro-management in your tournament.
Anyway, supply isn't the devil you describe. I have little faith on Relic today but COHO was a really good game that needed to be polished.