Hey Petter -
Thanks for the note.
One the first request there, the way to deal with video or HTML elements not being blank in the thumbnail is to put a graphic in the box that you're placing the element in. From the MIB's perspective, that space is a web browser (or a video player) so it leaves it blank, but if you put a graphic in there the way you would in any box in InDesign, it will preserve and export that for the thumbnail. Other folks do just replace the image in the folder structure later, which is a simple drag and drop - the key of course is to do that at the end of your workflow so it is not overwritten. But I can also talk to our plug-in devs about linking to a custom thumbnail preview either in the plug-in or the Prod Tool - we'd just have to look at level of effort against level of demand.
For the second one there, you're right that the plug-in makes popups as PNGs because they so often have transparency, and we don't have a force JPG setting because we found it led to too many support requests from people who didn't understand why their transparency went away. However, if you use the MIB Optimizer tool (iOS only) [http://support.magplus.com/entries/21868426-The-MIB-Optimizer-iOS-ONLY], one of its tricks is to go through all the image files in the MIB and look at the transparency channel in PNGs - if it is below a minimum threshold (I think 2%) it converts it to a JPG - so that would be a good way to get the file size savings - you can often reduce retina MIBs by as much as 30-40%. We've looked at building the same intelligent analysis into the plug-in export and found it made the export a lot slower, but we're always looking for ways to export better and smarter.