Yes we've always kept our long guns that way regardless if it's an AR or shotty. We train our members that way from day one and it's not an issue. It takes really no longer to get the long gun into play since you disengage the safety as you're acquiring the target. Also it has no wear effect on the springs that we can see.
I worked Google on this topic and most of what came back on cruiser safe showed that a lot of departments keep long guns stored like we do. I even found a lesson plan from the Arizona Department of Public Safety that teaches shotgun cruiser safe with the safety on.
Look at page 5
The main reason to teach using the safety for this method of storage is that you cannot go wrong.