Freedesktop.org mime-actions-spec states that default application for a MIME type is the one that is listed first for a given MIME type in section [Added Associations] of mimeapps.list, e.g.:
------
[Added Associations]
mimetype1=foo1.desktop;foo2.desktop;foo3.desktop;
------
foo1 will will be default for mimetype1

But if you choose an default application for some file in Thunar, it will be written to the end of the list.

I am not touching [Default Applications] section in this report. As far as I understand, it is needed to maintain compatibility between mime-actions-spec and xdg-open behavior. I am only covering [Added Associations] section misbehavior in Thunar.