A linear course and a branching course are two VERY different animals. With a branching course there are almost unlimited possibilities about how the user would progress through it and it may NOT be necessary for them to visit all slides. In fact it might only be necessary for them to visit a small fraction of the total number of slides in order to determine proficiency.
Since you're a web designer, try to imagine that someone wanted you to create a progress bar for a website you've built but where users are only likely to visit pages at random based on clicking links on the SiteMap page. You'd probably tell the client that creating a linear progress bar for such a requirement made no sense. The better way to do it would be to give the user feedback on the SiteMap page instead to show where they have been.
Instructional Designers don't think like web designers. They're very focused on achieving the learning goal (or at least they SHOULD BE) rather than just delivering content. That means the objective can be achieved in any number of ways, and the path is not necessarily linear.
My suggestion is that you may need to consider having more than one template for your Instructional Designers. One template would be a simple linear course. Another would use a main Menu slide linking out to a number of sections that the learner could complete before landing back on the Menu page each time. Once they have completed all sections, then more options appear to progress further. etc.