You may have a way out depending on price:
1. The general "owner occupier" exemption from stamp duty means that for a house under 125sq. mt. you must have a floor area certificate.
2. However, if the price is less than €317,500.00, then whether it is new or secondhand, you (as a first time buyer) are exempt from stamp duty. The FTP exemption does not rely upon the floor area cert. Also, I think that the €317.5k can probably be measured exclusive of V.A.T. (i.e. gross price €360k).
I haven't had this situation, but the above is my understanding of the law as currently stands, and this is an area of law in which I practice. Obviously you should double check with Revenue.
Hope this helps.