Probably just an earlier production run. There were a lot of "prototypes" of F14, though. A few clues I remember off the top of my head were the ROMs on the MPU have stickers on them saying "proto" (mine has these). Also, they will have wiring to the flash bulbs that were originally under the domes near the top right loop. Mine had the wiring, but it had been cut, presumably at the factory after realizing it presented a risk of shorting the MPU.
The clear domes you pointed out, as well as a clear center beacon, are from early production runs as far as I know.

Just checked my production number- 96080. So, mine was roughly 100 before yours and had the "proto 5" chips in it.
Another difference I remembered was that display board on prototypes had holes for 555 lamps. Mine has those as well, but again, I think some things from the "prototypes" ran over into regular production. My production date was 87114 (I think is November 4, 1987, which is 8 months into production, which is listed as starting in March that year.).

They changed them to white later in production. The number of minor changes that F14 went through makes it tought o tell what's a production game, but can roughly tell you where it was in production.