Directory view will not ignore blank lines
Basically I am still experiencing in version 3.20 the exact same problem described here: https://bugzilla.gnome.org/show_bug.cgi?id=695912 6 years ago
If the Preferences->Text Filters->"Trim blank line differences from the start and end of changes" checkbox is enabled, files which differ only by blank lines still show up as being different in the directory view.
From that discussion it seems the problem was fixed in commit 486aec, but I was not able to find that commit id in github.
I am aware that the bug report I reference above followed the discussion here: https://mail.gnome.org/archives/meld-list/2013-March/msg00033.html