The seated position, with the hips flexed, causes greater spinal compression on the lumbar vertebrae. Back Pad, vs. no back pad has nothing to do with that internal compression. Your glutes and lower abdominals are also less supportive of the spine in the seated position, making the spine weaker from this as well.
This is not a safer position, by any means, but if you have found a pain free method to press, go for it. Just understand that what is more likely is that the feel of the seated prss has given you a better stimulus for keeping your spine stiff than the standing press. I would still say take some weight off the bar and do them standing, but thats just me.