1. You can easily change the color of the border of the magnifier and secondary axis through the property 'edgeColor', which by default is set to black.
2. At this moment, the tool does not provide a handle at calling time. However, there are several supported Hot Key combinations that might be useful for your purpose. 'Control+D', for instance, can be used to delete the tool from the current figure.
Kris, thanks a lot to you too for your comments. In version 1.16, you could already switch from one inset to the next one in a figure( by pressing 'tab' of doble-clicking the inset to focus), regardless they are on the same axes or not.
Maybe this feature could already suit your needs.
I'm currently working on the performance issue, which is not an easy one. I'll let you know the status. Please don't hesitate to report any other issue/bug you might find.