I thought as much but wanted to verify. I have LE nr turned on with my D800e - but yah... that wait between shots for the DarkFrame is annoying! From what I understand though (and I could be wrong), shooting separate darkframes yourself to apply later works only if you are using the same exposure and settings for all the shots.
DarkFrame subtraction works best if you use the exact same exposure time as for the actual images, because with the same duration, the 'same' amount and locations of pixel-response-non-uniformity (PRNU) can build up as time progresses. Clever software can cheat a bit by correcting for different exposure times, but it's a compromise. Even better software than that can use an average of multiple
DarkFrames, to reduce random noise in the DarkFrame and only use pattern noise to remove from the actual images.
I'm not absolutely sure if RawTherapee does both of those clever optimizations (although it wouldn't surprise me), but it does allow to use a single DarkFrame for multiple images, which is more than most other RawConverters.
A separate DarkFrame is typically shot with lenscap or bodycap on, and the viewfinder covered, and the exposure time obviously set to manual.
Since heat buildup in the camera during long exposures can play a role, it also helps to use similar outdoor temperatures for the DarkFrames and try if shooting a DarkFrame mid-session works better than at the end of a shooting sequence. If the session is only a few images, it is also possible to shoot the DarkFrames at a different time.