I wouldn't go for the additional-hole idea...
Here's how I did it (MightyMite maple precision neck into WD Music precision alder body).
Once you can get the neck into the pocket (might require some sanding), just seat it well down and as far in (towards the bridge) as it will go. If there's a little side-side movement, try and hold it in the centre of the swing (a clamp can be handy here, or another pair of hands) and mark through the body for the four holes (a nail is fine).
If you mess-up (or want to double-check), just use some crayon or something to cover the previous marks, and do it again.
Drill the holes smaller than you need, and a little less deep, then use some smaller screws to bolt the neck on with the plate.
Use some wax on the screws, and back out if you think they might break!
Ensure that the screws are seated in the plate well, but not fully tight.
Then you just need to loosely string on an E and G string to check the side-side alignment (actually I used some fishing line, rather than strings, as I hadn't fitted the machine heads at the time).
If you need more movement, you can get some when you enlarge the holes to fit the real screws (just 'steer' the drill in the direction required) but I doubt you'll need to - the neck/pocket fit should be near-enough perfect anyway.
The real big no-no is overtightening and breaking a screw (don't ask me how I know...)
Other than screw-breaking (damn!) that approach worked perfectly for me, but get some more opinions!
Cheers,
Stewart