People really, really hate tunnels along public walkways or paths. They attract crime and can be downright intimidating for a lot of people. I think cyclists should be ecstatic that the pathway will be over the road and travel uninterrupted.
The option with the roundabout makes the most sense. Traffic heading onto Admirals off the TCH northbound is light and that light won't be changing very often. And quite honestly there's a lot of traffic turning onto McKenzie off the southbound TCH but it's not a crazy volume, either.
Like you say # 2 seems the best option except that the southbound lane from the TC onto McKenzie is down to one lane from two. It also appears that there are bike lanes on all roads, or is that supposed to represent the shoulder. I would like to see what the #2 design would look like if the east/west Goose went under the Admirals/McKenzie roadway, instead of over it.
Perhaps the best thing is to go to the Open House tomorrow and see a larger view of the designs and talk to the experts.