You might want to do a DNS leak test from your phone with the wireguard connection down and then with it up to make sure you’re tunneling DNS. This will be clearer if you set pihole to use something upstream that an ISP is unlikely to use - quad9 for example.
It’s probably still IPv6 related. If you use something like Network Analyzer on your phone while only connected to the mobile network you may find that it only shows an IPv6 address and DNS server, no IPv4 config. That could explain the difference. Particularly if you were using the maximum typically permissible MTU. Your provider might also be doing some 6to4 tunneling somewhere that adds overhead and causes size problems.