Yes, it can!
You can use more than one Checklist within your web application. Checklists can differ from each other in many aspects such as their;
Progression option (turned on or off)
Design settings, etc.
As you already know, you can't have two checklists with two separate Launcher icons on a single page. In other words, an end-user can't see two Launcher Icon at the same time, that belong to two separate Checklists.
That's why, if you want to utilize more than one Checklist within your web application, you need to target them to different pages or/and different user segments.
Let's assume you have two checklists: if their targeting and segmentation conditions intersect, this means that you're directing the two of them to the same pages and to the same users at the same time. In this case, one would override the other and you can see only one of them.
Thus, if you create two different checklists with different Launcher Icons or with different guides, be sure that either their targeting or segmentation condition is exclusive.