It is generally hard to say. A few bits and pieces are changing but nothing really substantial. It is very possible that your custom would just continue to work as it does right now. You could backup your /etc/pihole somewhere and then try the upgrade. If you cannot make it work, you can easily stop everything, restore /etc/pihole from your backup and go back to master with all components.
One major difference is that content in /etc/dnsmasq.d will not be loaded anymore by default - on one hand to prevent incompatibilities during upgrade but actually because there are still applications installing custom dnsmasq configuration that conflicts with stuff that is already present (remember the famous lxc.conf...). You can switch on importing custom config files through the config by setting
misc.etc_dnsmasq_d = true
either in /etc/pihole/pihole.toml or by simply running
sudo pihole-FTL --config misc.etc_dnsmasq_d true