I think using skyscanner or something similar should be a bit more transparent, they should have a * saying this price is available if you book with a certain payment type if this is the case. It is a bit disheartening to go to tripsta.com or another website from skyscanner, fill in your details and proceed to the payment page and have to pay 44 euro transaction fee higher than the price on skyscanner. The only cards available to me in Ireland as far as I know are mastercard and visa (debit or credit) so there is no way I can avail of the cheaper price.
A little drop down saying visa debit fee of 44 or 0 or whatever the cost on the skyscanner website would help me waste less time going to fill in details for flights I won't buy. If I knew that this flight had a payment fee in advance it is easier to judge what is the best and cheapest booking.
In the end I got a flight with no card fee