I copied the dnsmasq.conf from RaspAP installation into a new "yourname".conf file in /etc/dnsmasq.d
piHole installation backed up previous dnsmasq.conf (from RaspAP) in dnsmasq.conf.old and replaced with "conf-dir=/etc/dnsmasq.d". So I just created a new ".conf" file in /etc/dnsmasq.d and copied from /etc/dnsmasq.conf.old.
From RaspAP FAQ
For now, I can connect to hotspot with pihole. (extra tip: After newly added blacklist sites, restart pihole and flush client dns cache. If still not blocking, check whiltelist)