I think the immigration route that you have so far followed is rather confusing and making the whole situation potentially complex. Although I hope not.
It seems your fiance applied for an entry visa under current rules as a British Citizen.
Possibly because the EEA Family Permit route does not allow for fiance(e).
It is actually correct that technically when you are married you may be classed as a Family Member and that you may apply for a residence permit.
Under normal circumstances the Family Member does not legally need to make any application for a Residence Card.
For your reference the EEA2 application form for a Residence Card is here
The complication is this:- until you are married you are technically not a family member of an EEA national.
I've not come by your situation before. Normally the couple would be married before applying for entry to UK under EEA rules.
It's a tough call, but my suggestion, unless any member here can give first hand experience, is that you and your fiance would benefit from a consulation with an immigration advisor as to the best path to follow.
I do not suggest you discuss with UKBA until you have received legal advice first as I feel uneasy about possible comments from them.
Their issue will be the initial declaration by your fiance that he is a British Citizen, followed by a wish to switch to the EEA rules as an Irish Citizen. This is my concern.
The worst case scenario is that you will need to continue the route of spouse to UK citizen and pay for the FLR
The best case is that maybe you will be allowed to switch to Family Member and be allowed to stay without any costs.
Hope that helps to clarify.
