If you have what ANSYS calls a "Globally Unstable Flow", then flow instability is enough to create turbulent structures, so the effect of velocity fluctuations at the inlet is negligible. The fact of having two separate inlet is definitely a source of instabilities, and I guess that that Re>>1.
If you have compared your LES results with experimental data, that's perfect. However, if there is no experimental data available, it is always interesting to include velocity fluctuations to see if there is any difference in the numerical results.
In any case, I am curious about why are you having problems with LES + velocity fluctuations.