I think I understand what you are saying.
The thing to remember is to customise all your images before starting out on your book.
For best display in iPad 3 Retina, images in landscape should be 2048 width and height can be 1536 or 1496.
you should set your resolution before setting the size dimentions and check the constrain of whatever image processor used does not aler this. Any image bigger then 2 megapixels ( unless the recent updates changed this) will be flagged after you click "Deliver" and will need to be adjusted before you can move on.
After your images are iBA ready - if your page has a placeholder image & is masked... drag your image and drop into the placeholder - before "dropping" make sure you see the blue outline in the mask or the image will sit on top of and not in the mask and it will adopt the dimentions. After that you can juggle with the mask and or placeholder frame setting as you will.
Dragging an image and dropping outside of, or on a page without a placeholder mask - and your image will - as you say appear to be smaller. Open the Inspector at the rule icon =Metrics and it will show a size.. say.. 507 x 650. Look for the bar "Original Size" click that and it will show your images as..say, 2048 x 1536. Cancel that and return to the small images and pull it to the size you want to display or you can add a mask to the image and resize as desired.
Having jumped through hoops with this and similar image size and placings, I now set up a template and using 1 landscape masked placeholder image and one in portrait, I set the layout ( copy and paste the placeholder images as many as you require) and then drop in my chosen images.