Graph Fourier transform: the adjoint notation for the eigenbasis matrix
You terminology is something I am not used to.

$$ \hat{x} = \mathcal{F}_{G} x $$

If by $\hat{x}$ you mean the DFT (complex except very special cases), $x$ is your input (real or complex), and $\mathcal{F}_{G}$ is the matrix composed of the sinusoidal basis vectors, then your assertion that $U$ is real is dubious.  $\mathcal{F}_{G}$ is most certainly not.  With the proper normalizattion:

$$ \mathcal{F}_{G}^{-1} = \mathcal{F}_{G}^{*} $$

Now, for a known $x$ where $\hat{x}$ is known to be complex, how can $U$ be real?

Since they are using the complex conjugate, I would say that U is expected to also be capable of being complex.  I have not read the paper so I don't know where you picked up that assumption.