Configuring SciTE to automatically trim whitespace upon file save is super-easy! A minor tweak to the user.properties will tell SciTE to, automatically, trim spaces, tabs, etc. from the end of each line.
The following example is what I added to have it apply to my AutoHotkey files (which have an extension of .ahk). If you have file patterns you can achieve the same goal by using something like this: strip.trailing.spaces.$(file.patterns.yaml)=0