Don't see a question, but it appears from the information you provided that you failed to inform the board of the changes and built something different than what they agreed to. Now that you've been caught, what do you want? it's not the builder's responsibility to ask the Board for variances - the builder doesn't own the Lot and isn't a member of teh Association. Perhaps you need to read the covenants and find out what is required of you as an owner in a covenanted community.
This is not intended to be legal advice or create an attorney-client relationship. If more information is needed, you should consult with an attorney in your state regarding the specifics of your situation and the options available to you.