I've searched this forum for my question but couldn't find an answer. Hopefully Gunther can help. 

My question is, to make color grading easier in post, and to make it cohesive with other shots, it's better to shoot with a flat profile (Cinestyle, etc) to give more latitude for the color grade. Will shooting flat mess with the deflicker or any other function in LRTimelapse? Not sure if LRTimelapse uses contrast to determine the changes.

Alternatively, do you have any other suggestions or workflows that will help with color grading in post. I use a Canon 7D and it's native color is not what I usually like to see in my finished videos.

Love the program! Thank you.

A profile like that will only be applied when working with jpgs, which I do not recommend. I recommend shooting RAW, but of course you can have a flat profile (I use it on my nikons too) in order to get flat previews on the camera and a better histogram.
LRTimelapse doesn't care about that - only the camera previews will appear in this look, but once you go to Lightroom, Lightroom will develop the RAW files anyway and the profile will be gone (it's not needed anymore, since you will be doing the grading here based on the raw files). In the next step LRTimelapse will do the visual previews, where it uses the developed images as a basis for deflicker etc.