so you shot an auto exposure timelapse from day to night.
I will get to that in a sec. A suggestion, for the future, you can think of shooting manual ex in the day and let it fade to black as the sun sets. Than shoot a second night time manual exposure. now you have two sequences. Do a 3 sec dissolve between the two sequences.
Also when shooting in auto, only because you have too. Make sure you set your metering to evaluate so it is doing a large reading and not weighted or biasd. This way you will not get the popping as much as you have experienced.
No when it comes to grading. you are color correcting most likely the luminance values to get the sequence to play back seamless. You simply can do this with a levels or exposure node. Now the whole raw thing. Raw holds a ton of latitude before you than compress it out to jpeg format. In your case you do not need the raw images, and when shooting timelapse shooting just 2k jpegs will allow you to shoot faster as the camera does not need to buffer massive raw images that than get resampled to 1920×1080 or whatever your specs are for playback.
So convert your raw image seq to jpg. Batch process you 18 mega pixel images to 2k or HD, Import it in AE. do your color correction in AE. Bi pass your raw step as that is intended for folks who are doing heavy color correction and large exposure shifts.
I shoot raw for portraits and landscape. For a timelapse I shoot 2k, jpg, and remember to get motion blur even if you have to stack NDs on the lens. I shoot my timlapse in the middle of the day at 1/5th shutter speeds.
You can also try frame blending the sequence to blend out the pops.
Good Luck!