Hello, and welcome. I am a licensed attorney and happy to assist.
I'm sorry to hear about what has rightly been termed a fiasco, but happy to say that you do have recourse. Under the circumstances, I expect you will be able to move from the property when your lease expires, regain the amount paid for the security deposit, and have no liability in this, whatsoever. That includes financial responsibility in restoring the property to its original condition. Here's why:
First, while the Association controls what may or may not be done to the property, that is between the owner and the Board, only. The only potential involvement you would have could only stem from a situation in which you were actually provided with a copy of the governing documents before moving in, and ignored those documents to make changes not approved by the owner or Board. In that case, the owner would have recourse against you, but the Board would not. It's recourse would be and is against the homeowner, only. Add to that that the homeowner approved all of the changes and you have no legal security deposit issues, whatsoever. That is the case no matter how much the Board ultimately fines the owner for the changes that were made. Again, the owner made a decision as the owner of the property and all consequences that flow from that decision are between the Association and the owner, without regard to you.
You are not bound by an agreement to which you are not a party and of which youu were not aware, even if the CCRs originally prohibited the changes made, which it seems they did not. Again, all negative consequences in these circumstances fall 100% on the homeowner. If the owner refuses to give you back the entirety of the security deposit to which you are due upon moving, you can bring an action in court for wrongful retention of security deposit. The owner can be ordered not only to return the amount owed, but triple the amount of the unlawfully retained deposit as punitive damages.