I have 3 concerns about Articulate Presenter '13

This article should help you understand how your interaction is stored in your presentation and how they are saved.

As to your last question, the player was updated in this version of Studio, which only has one set of controls for Engage. I'm sharing an explanation by our community team below to help you understand how it works now and suggestions if you need something different:

To make up for some of the constraints of PowerPoint we created Engage. You get easy authoring because all you have to do is select a form-based interaction, add your content and hit publish. The drawback is that form-based authoring's simplicity comes with limited programming control, as well. It's designed that way on purpose.

 

Because Engage is a stand alone application, it has it's own navigation controls.

 

The original version of Engage had navigation controls that conflicted with the default player controls in Presenter. So when you inserted an Engage interaction you had two different types of players with different navigation. We had a lot of requests asking that we integrate the Engage navigation with the Presenter course player. And that's why we made the change because it's what was frequently requested and confirmed during our beta testing. Of course, as you note, the change doesn't meet everyone's need.

 

Essentially, the Engage interaction is content created in a separate application. So it has its own player controls and navigation. When you insert it into the PowerPoint slide you have to account for the Engage player settings chosen by the course author.

 

When creating an Engage interaction you have two choices:

 

 

1. Do you want Engage to have it's own navigation?
2. Do you want no navigation and only onscreen clicks?

 

Whichever you choose impacts how the navigation integrates with the player.

 

Solution

 

Currently there are three options when inserting the interactions into the PowerPoint slides:

 

 

• Insert Engage with the interaction's navigation controls and the course player's prev/next buttons are assumed by the Engage interaction. This lets you use the prev/next buttons to navigate through the parts of the interaction (and display each element in the menu). In a sense the interaction elements are treated as sub-slides. 
• Insert Engage with the navigation controls that were disabled in the interaction. Unfortunately that currently overrides the course's player controls and turns off the prev/next buttons because that's how the interaction was designed. Of course that leads to your frustration because you want to have the interactions act as a single slide with only onscreen clicks and still have the default prev/next buttons in the course player. That makes sense and we also submitted a feature request on your behalf.
• Insert Engage as a web object. Another solution in the short term is to publish the interaction any way you want. Change the name of the interaction.html to index.html and then insert the interaction as a web object. It doesn't take much longer. What you'll get is something similar to the way the interactions used to behave. You also have the means to customize the player color schemes to match your slide and create a more seamless experience.