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I've experienced a similar issue before. The problem is that the methods for getting the bounding box of an HTML/SVG element only work when the element is in the DOM and is visible. Instead of using visibility: hidden try position: absolute; left: -99999em on the div container element.
Steps to reproduce problem:
hidden
.80
.true
.What I expect:
A state that has a decent size for displaying on screen.
What I observe:
A state that has an okay label, but has a radius which goes far outside of the Paper region.
Also found someone having the same problem on Stack Overflow:
JointJS diagram drawn in hidden div has wrong scale - Stack Overflow
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