The rear door mounted carrier is easier to live with, as opening the doors is much easier.
Only a light box can be mounted on these, perhaps 20kgs or less of total weight. Assuming you are not carrying bikes as the same time.
It never seems a good idea to me to put boxes on these carries though.
I suspect their disclaimer of not using bike covers is to reduce drag when driving. The drag of a loose/flapping cover will cause additional force on the carrier.
I suspect you will be fine if you use bike covers, but ensure they are very well tied down to the bikes, to ensure no parts are flapping.