I have a fit issue in the helix area, don't know how they even passed QC and made it out the door.
You can see from the picture how the left monitor doesnt sit properly in the negative case mold.
Back to JH they go
Try wearing it without the cable attached, see if the problems still persists.
I had a problem where the socket was angled too inwards making it push against my skin.
I don't worry about it as long as you don't feel pain in your ear. It could be a good thing since you have a perfect seal.
As you can see, it has had no ill effects on me.
How much they stick out is not the important part, whether they seal properly and do not cause pain is what you should be asking yourself. If they fit and seal properly, it might not be a good idea to have them altered, as then they may not fit or seal anymore...