EVA's website/reservation system does not tie your PNR to your FF account if you decide not to credit to BR's FFP. As soon as you hit 'next' after selecting another *A FFP, it logs you out of your BR FFP and continues as a "Random Nobody".

Only mildly annoying for changing/viewing the reservation in the future as long as you have your reservation handy. Much more annoying in that it doesn't pre-fill the EAPIS info and you have to fill out manually what is automatic if you use BR's FFP.