The only negative to not having IR and RF at the same time (I set my remotes to both when I can) is for when RF stops working due to interference you can then still use the remote via IR (and troubleshoot over the phone). Of course you have to open the cabinet doors and aim. But your remote will continue to operate.

We had a client for about 6 months RF completely stopped working. He lived near no one, but a ski hill. System worked for years then some weird interference showed up for about 6 months. Had to use IR..... then one day RF worked as it should. Other than driving out to see the problem, since the remote was set to IR&RF no programming had to change. Our theory was there was some construction going on somewhere and the guys were using long range walkies or something causing the interference.