It's not that odd. Remember, M5 threads are standard only for forged dropouts. Due to the more complex (and expensive) manufacturing involved with forging, initially there were only a handful of manufacturers and a defacto standard evolved by the others copying the leader. In the case of stamped dropouts, the technology is much simpler. As a result, most the larger companies could afford to develop their own tooling for these dropouts and there would be much more chance for different standards to evolve.

A quick look at my stable indicates all 8 bicycles with forged dropouts use M5 theads. Of the 4 bicycles with stamped dropouts, 2 use M5 threads, 1 uses M6 and 1 has untapped clearance holes for M5 bolts. A quick look though some the old bicycles at LBS indicate a mix of the above and I even came across one with M5 in the rear and M6 up front! I suspect that if I continued my investagation, that I would come across some older, Imperial standards too.

The examples of M5 clearance holes were found primarily on the inexpensive, boom era models and it got me to thinking how M6 may have evolved. Since economy is a big factor on the entry bicycles with stamped dropouts, it would make common sense to save a few pennies by eliminating the tapping operation. The eyelet holes would therefore be designed to provide clearance for an M5 bolt, which was the standard for fender mounting. These holes could be punched as part of the dropout stamping operation (more expesive tooling but cheaper in the long run) or drilled as as separate operation (cheaper tooling, but more expensive in the long run).

After the boom, as the sales dropped off, companies started adding value to the low end models and one way to do this was by providing tapped eyelets. The evolution to six speed freewheels with tighter spacing between the small cog and dropout would also prompt a move to tapped eyelets, as the chain would be more liable to hang up the nut required for an untapped hole. The companies would be looking for the cheapest way to provide tapped eyelets. If the eyelets were punched as part of the dropout stamping, they could get by with not changing the tooling and simply tapping the M5 clearance hole to M6. For companies that drilled the eyelet holes, it was just as easy and cheap to change the tap drill size and produce an M5 tapped hole. Asa result both M5 and M6 tapped eyelets would exist on stamped dropouts.

Being one the larger companies, it is more likely that Fuji had the money to create their own tooling for dropout stamping and that they incorpated the eyelet punching into the tooling, as this would be cheaper in the long run. Consequently, the dropouts may have be intially produced for M5 clearance holes and have simply been adapted by tapping the existing M5 clearance holes to the next larger size, which would be M6. Of course, this is all speculation based on hindsight and a bit of reverse engineering.