The problem that i think we are going to have is like you said glueing.
I believe that an exact fit for the two is going to be hard for a
couple of reasons.

1)If you make the wood stem first, the glass is going to have to be
exact and you wont know that until it has cooled down. I suppose it
might be easier to make the glass first and fit the wood to it.

The second problem is, even though wood is dry, we all know that it
still moves with humidity and climate. A good idea would be to use a
flexible glue

For the glue, reminding you I am still new to turning, any clear clue
should work. If you have an experienced glass blower, they can put
colors in the glass specifically where they want. That said, the
bottom of the cupsounds like a wonderful place to me.