IMO, and JMO, but July 16th - referenced above - was still early days, relative to the expanding investigation. I say that because of the following occurrences in June and July, from the article you shared:
“RCMP also accessed Brooks-Murray's TextPlus account, a phone app she used for Wi-Fi calling. By the time police sought the records in early July, the court records said Brooks-Murray had "deleted the app because she doesn't need it anymore." Regardless, RCMP were able to access her account.”
“The documents also show Janie MacKenzie, Martell's mother, did a polygraph test on June 10. Her "physiology" was "not suitable for analysis" and no opinion was rendered.”
“On June 12, Cody Sullivan, the children's biological father, also did a polygraph and was determined to be truthful.”
“Cyndy Brooks-Murray, the children's maternal grandmother, and her boyfriend, Wade Paris, both passed polygraph tests on July 2.”
An investigator's comment states in a July 16 document that "because Lilly's boot print was confirmed to be a size 11, it is consistent with the boot print located on the pipeline trail in the search area."
I have no idea what the current prevailing theory is by LE, but I do think that the above quotes suggest they delved deeper into everything as time went on. JMO