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Is there a reason they are stacked from several pieces cut from the blank instead of one larger piece cut and glued at ninety degrees? Is it just not wanting to glue the end grain?

I’d say it has to due with availability of a solid 3” cube. Not sure where the idea of glueing the block at 90° to the neck shaft is coming from. I maintain the same grain orientation as the neck shaft.

Best, M

I guess the goal is to keep all the grain oriented the same. I glue two slices together and rotate 90 degrees so the glue line is vertical, but keep the endgrain facing the same direction so the heel-to-shaft joint is still side-grain. Just the growth rings are oriented differently, which I can't imagine causing any kind of problem. I would be a bit wary of gluing endgrain, but if you pre-coat with hide glue, let it dry, and lightly sand it back perfectly flat, it would probably be strong enough.

Depending on the heel design and neck blank thickness, my style sometimes needs to be widened out with a third slice, so when possible I buy shorter neck blanks and a thicker board of the same species for heels (which doesn't need to be high grade like the shaft). Or this one I used a maple wedge to create a contrasting stripe while widening the heel block.

Make sure the grain direction matches (preferably with wood from the same area of the same tree). If the wood pieces move differently with humidity changes, the joint will become quite obvious and even palpable. Matching grain minimizes this. End grain to side grain joints aren’t as weak as they are rumored to be, but I would never do that in this application. They are weak enough that the joint might fail, and the joint is much more likely to be noticeable with humidity changes.

Thought came from using bolt on butt joint, I put a dowel through the stack so the hanger bolt isn't just held by end grain. I've been making a few multi piece necks from reclaimed mahogany and I was thinking of ways to utilise extra pieces.

For what it's worth, I've never noticed any such bumps, and I have my guitars hanging on the wall year round in the extreme humidity swings here. That one in the photo does have some back cracks, though... invisible in the summer, but wide open in the winter. One of these winters I need to peel it off and reglue the braces in lower humidity.

That's what I figured you had in mind. I think the Stauffer "ice cream cone" heel has the grain oriented like that, though it looks too flat to use an end grain joint. I'd guess it has a tenon into the shaft piece.

If you want a more traditional curved heel transition, you'd want to put the glue line a bit down from where the heel flattens into the shaft so you don't chip off any short grain while carving. Around the red line here, where the curve is 45 degrees. Maybe a bit higher since the glue area increases as you go up, but so does the chipping risk. Green lines represent grain direction.

As always this depends what wood is available to you.
If possible I prefer to build the neck from a blank long enough to make the stacked heel, shaft and scarf joint and maintain a uniform grain direction.
If the wood direction is marked on the blank and the heel cuts are numbered and glued up in order and direction it will be difficult to to tell it is not one piece. Also if the scarf joint is cut by taking a triangle from the top of the blank, as opposed to just cutting the angle, it is not necessary to flip the head grain. This can avoid the change in grain direction which can make the joint so glaringly obvious, especially in mahogany.

It seems to me that a lot of the old methods were based on the idea that good wood was expensive, and hard to find, while labor was relatively cheap. Thus, on traditional Classical guitars, they would commonly use nominal 1" thick stock to make the neck, laminating the heel and using a V-join on the head. This avoided a lot of waste of stock at the expense of a bit more labor. In a production shop labor tends to be the most expensive input, so they try to minimize it.