I make goblets, and use a very shallow (1/16″ to 1/8″) tenon to align the stem to the bowl and base.
To drill these tenons, I use a 1/4″ straight router bit. These make flat-bottomed holes, which is important when the hole is only 1/16″ deep. A regular twist drill makes a pointy hole, and a brad-point bit has a point that will go too deep (and through the bottom of the goblet’s base).
I drill these on the lathe, with a Jacobs chuck in the tailstock. The quill on my lathe (Powermatic 3520B) has 16 TPI (threads per inch) pitch. That means that one revolution of the handle will move the quill 1/16″. I use this fact to measure the hole depth – advance the quill till the bit just starts to cut, then one revolution more is 1/16″ deep. Two gives me 1/8″, or 1 1/2 turns would be 3/32″, etc.