Alabama would be giving permission to marry to couples who qualify for marriage.
No they aren't giving permission, that is the purpose of removing the sanction. You don't have to obtain the State's permission to marry anyway, it's a fundamental right.
If a couple doesn't qualify, the state does not accept their marriage contract and they are not married in the eyes of the state.
No, if a couple does not qualify, they aren't administered a contract. This is also why the status of the contract has to be duly recorded, so as to prevent multiple contracts of this kind. This is part of the administrative aspect of the contract regarding civil domestic partnership, formerly known as "marriage." None of it has to do with the State sanctioning or endorsing the contract.
Let me make it clear again... The State of Alabama in no way endorses, condones, supports or sanctions whatever personal intimate arrangement you have regarding this contract. It is not responsible or liable for whatever you assume the contract is supposed to mean. What you choose to do with the contract after they have administered it, is your business.