We outsource our digital prints and they occasionally arrive with wrinkled backer sheets or other issues. We stopped having the premark applied in order to allow them to ship them rolled because they were otherwise a mess.
To the point, apply premark and tape a hinge on the graphic to the synthetic liner as if it were your substrate. Apply as you would to a substrate; remove the paper backer, lift, squeegee down to the synthetic liner, remove the tape hinge and trim.
Is it extra work? Yes.
Would do you end up with? A perfectly flat usable graphic with transfer tape applied on a clear, synthetic liner.
The only real problem is wasting perfectly good vinyl with synthetic liner in order to get the liner only.
If any knows where to buy a roll of liner only, I'd love to hear it.