Seems like the only way to change Diff options is via the main Diff UI (Tools -> File Difference).
But, diffing side-by-side appears in many different UIs (such as file history, Version control, etc).
So, one needs to plan ahead carefully - going to diff options and selecting what you want, saving, then invoking the UI which opens diff. (Tricky, with things like "Exiting with modified buffers").
The side-by-side UI should have a way to change options and update the diff display.
Some UIs have a SourceDiff/LineDiff button (File history).
Others, like Git->CompareWithRepo has "Re-diff", but not SourceDiff/LineDiff.
Sometimes when starting a diff Slick with pop a dialog complaining about encoding and/or line ending differences.
There are other seemingly random differences, like some UIs have the 'Undo' button, and others don't.
Sometimes there are 'Open' and/or 'Saveas' (Or save1 and save2) buttons - but not always, even in places where it would make sense.
Sometimes "Read only" checkboxes are available/displayed, sometimes not.
#1: There should always be an "Options" button, and when options are changed, "Rediff" should automatically happen.
#2: The various places that can open Diff should be made to be consistent.
They should all have the same set of options available, though in some cases buttons or menu items may need to be greyed when they don't make sense for some reason.