If it fits those cones then you need them, and usually cones go with with studs and not bolts.
You haven't answered what the axle is from, but I haven't noticed an original 48-53 Eaton with cones in the axle flanges. perhaps they did in later years, I don't know.
In any case, it doesn't really matter what the axle is from or why it has those cones when they are not expected... you either use them as intended or swap axle shafts for the plain ones with straight holes and bolts, but that's unnecessary if what you have works.
