From what you say there is no specific reason to work with percentages in Keynote as you are scaling images to a convenient size, not a specific enlargement factor.
I don't see how dragging handles will achieve this and I certainly don't want presized image holders.
Its very easy to learn how to resize images, select the image then click on one of the handles until is resizes to what you want. This is the main tool to position and size in Keynote and most other Mac applications.
Option 1:
Use the ruler to mark out guides to the position and pixel size you want, duplicate the slide as many times as you need to have guides in each slide. Drag in the images onto each slide and scale using the image handles. They will snap to the guides to help placement.
Option 2
Draw a rectangle shape and position and size it, then lock it to the slide (command L)
Drag in the images onto each slide and scale using the image handles, they will snap to two of the sides to help placement.
It took me just over two minutes to accurately place and resize 10 images of completely different pixel sizes, so this method is very fast and very precise. I hope to reassure you this method is used by the print, broadcast TV and graphics industry and I am sure will help you accomplish your end product.
