Firstly, the bolt holes are most probably just clearance for the mounting bolts/studs, so not intended for dowels or fitted bolts. YES, the holes should be a bit better aligned than they seem to be, but as already said "You get what you pay for" Peanuts and Monkeys and so on.
If a swivel base, I would set the vice at 0 degrees to the base, and then open up the offending hole(s) a little.
As already advised, clamp a parallel against one side of a Tee slot, invert vice, clamp to parallell, and open up the offending hole, preferably with an end mill or slot drill .
If possible, mill a slot for a key, across the base, and drill and tap for securing screws.
Once aligned, right way up, make a key to fit the vice, and to be a snug fit in the Tee slot.
If this is not possible, make an alignment fixture, ready for future use.
Turn the bottom end of two pieces of round bar, to be a snug fit in the Tee slot, but not long enough to protrude into the Tee nut area, (and tall enough that a horizontal bar can be clamped in the vice; eventually)
Drill through to take long bolts (preferably) or studs, to engage with tee nuts in the slot.
Fix the horizontal bar to the two verticals, at such a height that it clears the base of the vice jaws, but so that material needs to be removed from the vertical plane, to allow the vice jaws to clamp on to it.
Having now made a sort of "goal post", (ensuring that the parts cannot easily move relative to each other) clamp it to the table. Using an end mill, machine the face that will bear against the fixed jaw of the vice, removing material until the vice can be clamped to it, with the vice fixings in place, but not tight.
You may need to offer up the vice, a few times, to get the correct position.
If you want to, machine a little material off the face that will be contacted by the moving jaw.
Now, to align the vice, it is laid on the table, over its fixing bolts (left slack) and the "goal post" fixture is clamped into the Tee slots.
The vice is now clamped to the horizontal member.
When the vice holding bolts are tightened, the vice should be correctly aligned.
Slacken the vice, remove the "goal post" bolts , "goal post" and its Tee nuts, and the vice should be aligned within a thou or so.
This saves me about 15 minutes of clocking, winding and tapping to and fro, when I replace the vice on the table of the mill.
It is not my original idea, just a variation on a time saving idea published some time ago.
Howard