It's probably an individual thing, but in my own experience, having weight on top of the rack is not a big deal, if you don't make it one. You adapt. You get used to it. It becomes second nature, or normal. Same with panniers.
(The exception is when you use very heavy loads, and you have a wobbly rack or mounting system. Not good. Fortunately, though, it's easy to avoid this with a good, solid rack and secure mounting.)
****
Someone mentioned backpacks that have built-in hooks, so they can be attached to the racks just like panniers.
****
I've used panniers quite a bit, and they are good in many ways; but there is always a slight inconvenience loading and unloading.
The exception to this is when the pannier is extra large, and the backpack slides in and out easily. Then it's not bad at all.
The Xtracycle system is quick -- as with the milk crate, you can just set something down inside.
There are open-top panniers and wire racks that allow for the same.