What PDF viewer are you using to view the MP4?
We're using Acrobat Pro CC 2014 v11 to view the PDF, but my client will be using a standard Acrobat Viewer
You can control the quality of the video (aspect ratio, pixel dimensions, frames/minute, etc.) by using the Adobe Media Encoder which comes with InDesign CS5 or later installations, including InDesign CC. InDesign only includes what you have placed and passes it on to the PDF file. There are no video quality controls in InDesign.
You cannot change the way Adobe Acrobat or Adobe Reader displays the MP4. If you don't like the way Acrobat/Reader handles display of a floating window, then you'll have to display it within the page. For more info, inquire in the Rich Media Acrobat forum.