I think your expectations are slightly wrong.
You need to understand what the web interface considers a "custom" server and how they are counted.
When you enter a "Custom" DNS Server, this server is added to the list of upstream servers. There is no real difference between "Custom" and "Normal" upstream servers.
There is only one list of servers, but we show some common upstream servers using the checkboxes:
The servers marked on the top with checkboes are not counted as "Custom", but they are active.
You are using 4 known (and common) servers:
[dns]
upstreams = [
"84.200.69.80",
"2001:1608:10:25:0:0:1c04:b12f",
"208.67.222.222",
"2620:119:35::35"
] ### CHANGED, default = []
They are not counted as "custom" because all 4 items are showing on the top, with one checkbox for each server.
Maybe we need to change the text, but your Pi-hole is using 4 upstream DNS servers, as expected.