IMO:
If:
The clump of 2 different child-sized boot prints (which IIRC, the RCMP stated were coincident with their actual boot sizes) were not "planted there" on the pipeline trail by someone purposely as "false evidence" they had been on foot there that day/recently...
Then:
An adult with average or greater upper body strength capable of carrying them a distance to their vehicle, could have first subdued Lilly and Jack at or near home, and then driven them to the pipeline trail and dropped them off there while they were subdued but still alive. And the boot prints were actual physical evidence of them struggling to get free from some type of physical encumberance.
Such as:
If they were already subdued by drugs or physical violence at or near home (or even believed to be completely unconcious or deceased by someone who in a panic or not miscalculated the level of subduing) they could have then been "contained" -- e.g., rolled up in rugs, carpeting, sleeping bags, tarps, bedding, adult-sized clothing, etc. -- for transport/the drive to the pipeline trail location of the boot prints, and dropped there where they regained conciousness and/or were startled awake by being dropped from vehicle height with enough force to make the imprints in the soil, and they could have made those prints as they were fighting for their lives trying to wiggle their way out by their feet of whatever they were wrapped in if they were dropped there.
IMO, it's possible, if this occurred -- foul play by an adult with access to them/their home/property who subdued them & took them away in a vehicle -- that it was a dropoff point far enough from people at home and/or in the neighborhood for voices and/or sounds of human struggle such as crying, moaning, screaming to go largely unnoticed, and it was a chosen location where they had more privacy where they could do whatever was done to them in a more isolated setting.
If this scenario is one explanation for the bootprints to be there and they were Lilly and Jack's from while they were alive but captives, it tears me up to consider the possibilities of what could have happened from there... but they could have been further subdued there, and taken anywhere near or far.
Linked to this line of thought, i's always been a concern of mine that per RCMP personnel onsite that day, as stated in MSM linked way upthread -- that when LE told their mother where they were searching for Lilly and Jack and said it included along the pipeline trail -- she reportedly immediately reacted with heightened emotion & ran back to the house & was inconsolable after that (paraphrasing) & left soon after with her mother, never to return.
If her reaction to the search location including the pipeline trail was the way it seems, it has always made me wonder if there was significance that hit her on that location, as to it being possibly a frightening prospect if she thought they may have gone or been there...
Perhaps there was local wisdom about it or a sense of it being a location where bad things could happen or would be threatening to lost/wandering children in some way or where they weren't allowed to go because there was danger of falling into icy waters.
I just don't know if it makes sense in that frame or is totally off the mark for her to have reportedly reacted like that.
JMO