Don't expect any fix soon, this bug report (and all others I've reported) was totally ignored.
Fortunately, you can fix it yourself by copying the file "transpose.py" from the Default package (this is for Windows, it's a zip file):
C:\Program Files\Sublime Text 3\Packages\Default.sublime-package
to your user folder:
and change the default value of "can_transpose_words" argument to True:
def transpose_selections(edit, view, can_transpose_words = True):
The drawback is that you override the standard source file and you have to check when ST is updated if this source is modified.