Personally I like to have a lower level so i can see water movement and have a quick and easy indication of positive flow.
There is no reason not fill it all the way if you prefer but I would leave a slight air pocket maybe above where you can see to absorb pressure changes in the loop.
There should be no issue with bubble formation as the return line should be connected to a bottom port or if its a top port it should be fitted with a drop tube to stop any fluid above the res from draining into it, potentially causing an overflow.
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