This isn’t possible in ST3 except possibly through a third party plugin that does some sort of tracking on edits to know where you’ve modified the file so it knows where to trim. I’m not aware of anything that does that though.
However, ST4 has enhanced white space trimming options available as outlined below. Builds of ST4 are currently available to licensed users only and are being distributed on the Discord Server currently.
// Controls where trailing white space is removed on save.
// - "none": Do not remove any trailing white space on save.
// - "all": Remove all trailing white space on save.
// - "not_on_caret": Only remove white space that won't affect the caret.
// When used in conjunction with "save_on_focus_lost" and
// certain desktop environments that frequently make the
// application lose focus this avoids the caret jumping
// around a lot.
"trim_trailing_white_space_on_save": "none",
// Only trim white space on save for the parts of a file that have been
// modified by you. If there is trailing white space in other parts of the
// file they are left alone.
"trim_only_modified_white_space": true,