Possible scenarios, based on what we know:
1) Something happened at Stone Pacific after Ben was seen on the CCTV. A possible altercation or 'intervention', where the 'perp' hurt Ben in his van, drove the van out along Lake Cowichan Rd and dropped him off (perhaps up the Youbou Logging Rd); drove back toward Stone Pacific, parking on the side of the road and hoofing it back to Stone Pacific. This scenario does not work, as the dogs picked up Ben's scent leading from the van. (Did the dogs pick up Ben's scent specifcally, or was it simply the scent of someone walking away from the van?)
2) Ben went to his next job (do we know if he had one and where it was??) where something happened. They dropped him somewhere and then took the van back toward Duncan, so that it looked like something happened on his way back to town. (Which way was the van facing when it was found??)
3) Ben had an accident at the job earlier in the morning, hitting his head. He thought he was o.k., but he wasn't. He dropped the keys back at the Stone Pacific office, then drove around for a while, eventually getting disoriented and naseous. He pulled over to the side of the road to puke. By then his disorientation was increasing, so he wandered off, confused.
4) Ben dropped off the keys at Stone Pacific, and then headed off for another quick job. He had prearranged a meeting/pick-up at a spot along Lake Cowichan Rd. He smashed his phone, so he couldn't be tracked. He left the vehicle running so that it was found under suspicious circumstances. He trekked back toward Stone Pacific, where his "partner" in escape from his current life was waiting to do exactly that.
I'm sure there are other theories.
One thing that seems very unusual in this case is that it is the SAR team that is speaking to the media, simply about their searches. LE is not the one holding press conferences. They seem to want to keep things under wraps, indicating that they have a strong theory in place already.