When ARP or whoever designed/choose the studs and nuts for the Miata they obviously did that before the NB windage tray was invented. The ARP nut and washer has a higher profile than the OEM bolts which makes it interfere with the tray. I have seen other people commenting this on miata.net and mt.net.
I choose to fix this by drilling holes with a bunch of worn out drill bits. 1 hour of swearing and I had a molested tray that fits. Not good for rigidity but better tan running without the tray.