You can still tell which is which, although not from the hoods. No spoiler is an SE, unless it has the Rallye stripes, which nobody else has. Single exhaust is a giveaway on the SE.
RT has the hood to fender stripes or no stripes, and body color spoiler.
SRT has the black spoiler, SRT stripes, and SRT wheels.
I just saw a Challenger on the road yesterday, which is still pretty rare, and saw it was blue so no SRT, then I thought "hm, I wonder if it's an R/T or SE..." So I looked, and no spoiler = SE.
As mentioned above, it's certainly possible to disguise on model as another if you want to, but at least off the showroom floor it is distinguishable.