Just to close things down...
Draw.io HTML embedding works perfectly well on a "simple" web-page; though the fault is not intrinsically with
draw.io embedding code, it does not work reliably when there are divs that are not initially visible, a problem exacerbated when divs are nested.
The incompatibilities of embedding and hidden divs are browser dependent and lie, ultimately I believe, with the fact that div properties, particularly height and width, have not stabilised at the time the embedder javascript runs, leading to diagram sizing issues (amongst other things).
The worst possible approach to hiding divs is to use display: none; the least bad is to clip to a zero sized rectangle, but even that does not always eliminate rendering issues, or, particularly in the case of IE11 (in Edge or IE10 modes), misplaced zoom controls.
The ultimate solution is therefore never to embed a diagram in a hidden div; if this rule is obeyed everything seems to work fine.
My solution to the need to hide divs (for large and complex articles, especially if they are to support RWD for viewing on mobile devices) has been to use a little javascript and to add an event listener for the window to trigger div hiding once the page has loaded (I continue to use clipping and have not checked whether going back to display: none becomes viable - I don't see why that shouldn't work though). Whilst this is a bit inelegant, and the render shows everything before it is then hidden, it almost looks like a page preview given that the hiding uses animations, so quite acceptable.
I remain absolutely delighted with
draw.io's capabilities and the quality of the implementation and I'm very pleased to be able to use them and link to other articles from objects in an SVG diagram.
You can see results
here (without links in the SVG) and
here (with clickable links in the SVG).
Results are good and consistent in desktop FF, Chrome and IE (with the minor exception of superfluous scrollbars in IE only), and in responsive views emulating mobile devices in the three browsers. In real life, the zoom boxes are sometimes misplaced in the Android Internet browser on my Galaxy S4 - but they are OK in Chrome.
Best regards, Julian