The dome was designed in 1979. They did not design it with cup holders in mind. It was not designed with individual seats in mind either. They wanted to fit as many seats as they could in a very limited stadium footprint.
That said, when I have sat at CitiField, my cup holder was built into the arm rest. This was the option Syracuse considered very strongly before eventually rejecting.
Here is what they look like at CitiField. I believe they have multiple types of seats there, like we will soon have.
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