In presenter mode, the #presenter-mode-zoom-container element wraps the whole page content with a zoom: 1.5 style applied. This increases the size of all elements on the page, including iframes rendered by Connect macros. However, the zoom level only affects the size of the iframe itself, it doesn’t have any effect on its contents.
The AP bridge automatically sets the height of the iframe to the height of its content. For example, if the iframe content is 150px high, a height: 150px style is set on the iframe. However, due to the zoom: 1.5 style, this height is scaled up to 225 px, causing a white gap at the bottom of the iframe.
I believe to fix the issue, a zoom: 0.666 style would need to be set on Connect iframes, to undo the zoom level of the presenter mode. In addition, it would be nice if the iframe was somehow informed about the zoom level so that it could apply it to its own contents as well.