Danial,
It is easier to do a clean hole with a Forstner bit.
For one it is easier for the point to be in the right place, and so the axis of the hole, and sides of the holes are in the right place. A twist drill is somewhat of a mongrel.
Once you have 2 holes in two pieces of material that are in the right place, then the floating tenon will have them aligned without having to sand, or plane material off the sides because they were misaligned.
I would suggest doing what Steve suggests. Get a few pieces of wood and layout where the holes should be.
For 2 of them use a forstner bit, and for the other two use a twist drill.
Then see which ones give a more accurate alignment and a tight fit to the tenon or dowel/rod.
If the twist drill works for you, then you know...
If the Forstner works then you know that.
If neither work, then you also know that too.
The flat bottom does make it easier to know how long the dowel should be (or how long is too long), and when the depth is shallow you get maximal side area as you are not losing the depth from the cone from point to the side.