Testing about with this when i was double checking things, that few seconds for an item to pop up is enough to kill, especially if you are flying and its a tree
Here is the possible combinations you can do to avoid popups and other things like that. (Yes being that its ok, no being that its not ok):
DVD/HDD - Yes
DVD/USB - Yes
USB/HDD - Yes
HDD/HDD - No
USB/USB - No
As stated there was no patch stated to fix this, its a bandwidth limitation issue, you can't patch that as it requires new hardware, there will never be a fix to allow both from the same drive and keep popup gone. I can't be arsed to find my big long post on this but for example say the dvd drive can do 1gbit of bandwidth per second and so can the HDD, combined you have 2gb/s, using both discs on one thing you are limited to the 1gb/s however, this is whats happening and why its required to install one and not the other or install the other to another drive.
For a really basic analogy think of it as trying to condense two lanes of traffic to one, its never going to be as fast as it was with two but it will still work with some issues of things having to wait to move over and get through.