Yes. You put any optic behind the sight (your eyes for instance) and the reticle still has the same angular dimensions. This setup you describe was anticipated and intended by EOTech.
Of course, the reticle, like any BDC system, only works for a given trajectory, so your results may vary. It's all a matter of getting used to where your rifle/load combination shoots at various distances.
We have a RRA (Rock River Arms) 16" bbl HBAR "M4gery" here for UltiMAK product testing, and we've mounted this combo on it, as well as with the 4x EOTech magnifier and the Aimpoint 3x Mag.
That being said, there IS a problem with height alignment-- the EOtech magnifier mounts (at least the QD ones we have here) align with the taller 553 sight, so the standard height sights are a bit too low for the magnifier. It works, but it's sub optimal. The solution is to use the Aimpoint Magnifier on the TwistMount with the QRP spacer. THAT makes a very nice combo. I've set up several EOTech/Aimpoint combos for people, and they all loved them.