I use the Modern Style for Start10 and I like having the Settings link on the right side so it's always available but I didn't want it taking up a slot in my All programs list. I couldn't find another solution here in the forum to do this so thought I would share what I ended up doing to make it work for me.

- If you just delete the default C:\ProgramData\Microsoft\Windows\Start Menu\Programs\Settings.lnk shortcut from All Programs, it breaks the Settings link on the right side as well (the right side link really should be separated IMHO but that's for another topic.) So that was a no go.

- My next thought was to set the shortcut to be Hidden since Start10 won't display hidden shortcuts (which is great) but the default Settings.lnk for the left side doesn't allow the Hidden attribute to be set to it directly with out adjusting security settings which I didn't want to fuss with after every update.

- In File Explorer, I ended up deleting the default C:\ProgramData\Microsoft\Windows\Start Menu\Programs\Settings.lnk shortcut (All Programs location) which as mentioned above did break the right side link. I then created a new shortcut by Right Clicking in a blank area of the File Explorer window, New, Shortcut. In the New Shortcut dialog, I set the location for the new shortcut to ms-settings: and clicked Next and Named the Shortcut Settings and clicked Finish. I then right clicked the new shortcut and selected Properties. I then could use the General tab to enable the Hidden flag for the new shortcut.

The nice thing about this setup is that the new shortcut is a .URL shortcut vs the original .LNK and if a future Start10 update pushes out a new Settings.lnk I can easily delete it to remove it again and my new hidden shortcut should continue working as is. Hope this helps anyone else who might be looking to do the same or if someone knows of a better method would love to hear about it. Thanks! 

Now to figure out how to change that Universal Apps folder icon.