As both a recreational and distance cyclist, I find the SBHT a big improvement over riding on M-109. I find a paved trail is nearly always better than sharing the road, because it’s hard for big trucks to share and cars don’t always feel the need to.
As for the main topic here, I don’t see the problem with routing the SBHT around Glen Arbor. Many trails skirt towns, but the downtown is either visible to cyclists or a sign points us to it. We can either visit or go on past without getting tangled up in local traffic. Plus we don’t have to worry about the crowds of pedestrians on Western Ave.