I concur. A proper ATMOS setup needs the bed layer (fronts and side / back surrounds) at ear level. Having everything in ceiling will not yield proper results for ATMOS so those two speakers can be skipped. If this is a new install, maybe run some wires to the ATMOS location in case things change down the road.
People often underestimate the difference that good subwoofers can make. The R-100SW may still be available but the latest iteration is the R-101SW. The spec sheet rates that sub only down to 30Hz. The RF 7-III is rated down to 32Hz so those little subwoofers add almost nothing! If you run the front speakers full range the subwoofers are literally a waste of money.
If this is for home theatre you want to target a sub that gets closer to 20Hz in the frequency response. As suggested above, add the cost of the ATMOS to your budget and look for better subs that will dig deeper than your tower speakers. Two are preferred to give you smoother bass response throughout the room, but those towers go pretty deep already and I would lean towards one really good sub over two weaker performers. If budget doesn't allow two better subs you can always add a second one in the future.