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I have a '73 with the factory hardtop which is clearly indicated on the tank sticker. It came with the same pins as the soft top, but as stated above it took a bit of tweeking to get them to engage and release smoothly. It nor either of the tops on my 1963 have ever let go, although at 150mph in the '63 with the soft top up I could have used ear plugs... sorry it's a long story.
I have also seen quite a few with bolts inserted in them. Frankly they do appear much more secure and have considered using them myself.
If you want to have a few laughs, go to the Miata Forum and listen to them recount the tales of their soft-tops coming unlatched at speed. Some of them are hilarious... even if somewhat less destructive.
From the comments here, it sounds like the bolts were the way it came from the factory, with the possible exception of 1968, where they may have changed from the pins to bolts. Who knows, maybe the dealers made the suggestion that pins be added to the hardtop for convenience.
I can see people changing the bolts to pins for convenience. If you were removing the hardtop quite often, then the pins would come in handy, because bolting them up is a PITA.
The easiest way to bolt the hardtop on is to do it while the deck is in the open position. Have someone (or two) hold the hardtop in position while you screw the nuts onto the threaded rods. Then slowly close the deck lid, push down until you hear it click, screw in the two side screws, and finally latch the front into place.