So this issue is a permissions issue. When running IE in EPM mode, regkeys are being blocked at location HKCU\Software\Microsoft\TabletTip\1.7 due to ALL APPLICATION PACKAGES not being added to permissions. So a way to fix this (please respond if this does not work), is to go to
Win key
type "regedit" and click on the regedit application
Navigation to HKey_CURRENT_USER\Software\Microsoft\TabletTip\1.7
Right click on the 1.7 directory
Select "Permissions..."
Click Add
Click Advanced
For Locations choose your computer
Click Find Now
Select ALL APPLICATION PACKAGES and click OK
A fix will be coming down, but in the meantime, this is correct fix
Yep!. It's not in the core 'Settings' pane, but rather part of one of the core packages. Open up the settings view (Mac: Atom > Preferences), select 'Packages' from the list on the left, and find the whitespace package (type "whitespace" in the search box under Installed Packages:
There's a checkbox to disable the auto-removal of trailing spaces under that package's settings:
Best Answer
For temporary solution or for someone like me permanent solution: