Somewhere here I posted that I installed the Rally Armor UR flaps. Those come without any holes and have to be trimmed. It sounds to me that the flaps you got may be for the 4 door sedan which would be different but how much is unknown to me since I never installed a set of those. Anyway, I did need to purchase a set of hardware for some 30 bucks I think, from Rosenthal/Finishline. I asked them for all the hardware required to install OEM Mazda mudflaps on a stock 2. They shipped a bunch of hardware all longer than the stuff I removed. I had to match, mark and drill holes in my new flaps.
The Fasteners you describe work by going through the flap and then through the fender liner then through whatever sheet-metal or plastic the fender liner originally attached to. This is why the longer hardware was required.
Hope this helps. If not, sell it and buy OEM at a discount from Rosenthal/Finishline.