After a quick play with your nice ISO I do see that the MX-tools Qt-apps, work fine within a LXQT session and do use the kvantum defined theming. The issue is with gtk settings, which are not setup properly or not recognised by GTK apps.
You can either fix this through xsessiond or copy/adjust the corrensending "gtkrc" files:
~/.gtkrc-2.0 and /etc/gtk-2.0/gtkrc
~/.config/gtk-3.0/settings.ini and /etc/gtk-3.0/settings.ini