I thought so! There are a lot of little quirks with travel. Usually I get scanned by the Feds landing at New Atlantis, other times I don't. Sometimes I can jump straight to surface other times I need to go from orbit. Just little things I haven't paid attention to so I can't say definitively what the criteria is. But, jumping from the scanner is a way nicer way to do it. I just got in the ha it of traveling from the quest menu because I can go from planet surface -> new system -> planet surface with one action (usually).