Russ. Four bolts would make this easy, just slide the box sideways, locate, bolt up. Studs are traditionally used in soft castings to alleviate wear on the soft threads in situations which require fastenings to be released from time to time, so why BSA used a mix of studs and bolts here is a conundrum. This is what I reckon.
With bolts, there is always the danger of bottoming, so they will err on the side of caution and be short, this does not matter for the top fixings, in that the gearbox flange is compressed against the crankcase under load. The bottom fixings are in tension under load and will require the maximum purchase and full utilisation of the crankcase threads, hence the use of studs, which can be gently bottomed to use all the available thread.
The easy way to assemble is to make sure the threads are free running and nice and clean, then tape wrap the input shaft splines to protect the seal. Grease the seal and position the box loosely with the bolts, and add the studs through the mounting flange. Finally fit the stud nuts. Check all is positioned correctly and nip them up. Cheats like me slot the stud ends, and use Loctite on all threads. Plus the usual washers.
Fitting the studs first is OK, but risks damaging the seal as the box has to be skewed and manipulated to clear the studs. As Morris says, without the mainshaft it is dead easy, gives a bit more choice, but a pain if the box is already assembled and has to be stripped just to pull the shaft.
Swarfy.