Indian factory tried changing the oil flow into the clutch pack in order to reduce gear grinding. My guess is that was late 26 - early 27 in the early stages of developing the 45ci engine.

The meaning was that the clutch gear by its spinning motion should scoop up oil and transport that via a channel in the middle case that continues with the curved channel in the sealing area, seen in the one of Lukas picture of the gearbox. The motion was meant to overfill the gearbox so the excess oil would flow through the drilled hole in the mainshaft into the center of the clutch pack, and the oil centrifugal force by the spinning clutch would help separate the friction discs.

It did not work as intended, it did not solve gear grinding. The later version, your "set 2", the Indian factory reversed back to undrilled mainshaft and the 2 large holes for eqalising oil level in the primary and gearbox. I guess that revision came late 27 or early 28, as the early version, your "set 1", is quite rare.

Clutch covers with different height of the oil level hole can be found but I don't know when changes where implemented. I would guess without knowing that the clutch cover with the level screw higher up, really is for the  "set 1" gearbox. 

A revision of the clutch pack was released in Augusti -28, so the factory did work continously to improve clutch release and slip.

Earlier short frame scout gearboxes can be found with either one or 2 oil level equalising holes. For all I know they or the Chief did never have drilled mainshafts so this "set 1" was a short lived Scout experiment from the factory.