Thanks! I also prefer "non-default" or maybe "mismatching" ("non-matching"?) to "different".
I don't know if the option should be "only show mismatching" (which can be turned off from the menu when the user selects to hide EOL) or "always show mismatching" (with the menu option enabling also matching ones). (Then again, with this option available, "show every end of line" doesn't make much sense to have, and users will more likely want to choose between the other two, so your current proposal is probably the best.)