Backflip/Gator/Extang type tonneau cover with OEM plastic bed liner?

[2016LTZinFL]

Looking to install a trifold, flush mount tonneau cover. There are a few I like and all sit inside of the bed and are flush mounted. The main area I am concerned with is the front of the bed where the plastic bed liner comes up over the lip of the bed. Will this be a problem with the flush type of cover I am wanting to purchase. My only other option is the Extand 2.0 that sits on top of the bed and does not have rails. I like the flush look better. Anyone have a plastic bed liner and a flush blunted bed cover?

[TimmyG]

Should work with a bakflip

 

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[Doobs41378]

I have a Bakflip HD and they did have to put something in between there so rain did not get between the liner and the cover.