Problem finally solved.
I found a thread on my ISP forum with a guy that had exactly the same problem as me (but with IOS).
The solution is to modify the IPv6 prefix delegation on the ISP router and add a next hop to the primary prefix. I decided to add the own ISP router prefix as a next hop and now the router is not spreading IPv6 DNS anymore. And all my devices are going through pi-hole.
Thanks for your help.