This has been a recurring problem in our apps. Not only does it make the UI look inconsistent with our other dialogs, it also makes our code inconsistent because of the largely different way how we have to handle the buttons in the dialog footer, and it is really painful to work with AtlasKit components that are not adapted to small viewport sizes (such as dropdowns and inline dialogs) when the size of the iframe is restricted to the dialog body.
While experimenting around, I have found a workaround for this problem, which I want to share here for anyone else who comes across it.
"height": "100%" and
"width": "100%" in the macro editor settings in the connect app descriptor, the dialog is suddenly opened as a fullscreen dialog without chrome (header and footer). I am pretty sure that this is not documented and that it also didn’t behave like this before. By making the background of the iframe body transparent, we can then use the AtlasKit Dialog component to render our own dialog, with full control of the dialog header and footer.