I also have this problem when I use nm-dnsmasq and connect to work over VPN.
Although there is now a /etc/NetworkManager/dnsmasq.d directory, adding a file there with "strict-order" in it is not enough to fix the problem. That option seems to have no effect when addresses are conveyed to dnsmasq over D-Bus.
So I now work around the problem by commenting out "dns=dnsmasq" in /e/NM/NM.conf.
I also have this problem when I use nm-dnsmasq and connect to work over VPN.
Although there is now a /etc/NetworkMan ager/dnsmasq. d directory, adding a file there with "strict-order" in it is not enough to fix the problem. That option seems to have no effect when addresses are conveyed to dnsmasq over D-Bus.
So I now work around the problem by commenting out "dns=dnsmasq" in /e/NM/NM.conf.