Quick answer: No you lose nothing in that radio by going to an aftermarket unit.
I am in the process of getting all the items needed to install an aftermarket head unit in an RTL myself. Been reading the Pilot, civic and Fit forums as that same radio is used in all of those LX trims. The 5" radio has NO extra functionality in the vehicle aside from bluetooth phone, a display for the backup camera, one USB jack for a phone or memory stick, and the stereo itself.
The stereo I am getting is a Pioneer AVIC-8100NEX and it was last year's top of the line unit. It can be had on the net for about $900 and with all the steering wheel control interface and plug wiring plus dask mount kit, you are in at $1100. I will be installing this myself so no other costs involved.You lose zero of the Honda features.
To me this gives a much nicer 7" touchscreen stereo with all the cool android auto, navigation, voice control, apps, and much better sound than the Honda unit. Not to mention the display face pivots to give a better view, it plays CD's and DVD's, accepts SD cards, has dual zone rear video and sound outputs to a rear monitor for my kid, it has less glare and does not retain fingerprints.
I did not need the LED daytime running lights, side camera nor the lighted vanity mirrors that are the only real extras you pay for to get the RTL-T. I will have more stereo technology in my RTL for less money that those with any of the higher trims, and I will have less issues as reported by users here with their buggy Honda head unit.