It doesn't seem useful to always add the proxy setting to each connection profile that supports IP configuration. This normalization requires additional code and especially, it creates a new empty section in every new keyfile:
# nmcli connection add type dummy ifname dummy1
# cat /etc/NetworkManager/system-connections/dummy-dummy1.nmconnection
[connection]
id=dummy-dummy1
uuid=8dd2bb73-b338-428f-ad6d-082c37a58566
type=dummy
interface-name=dummy1
[dummy]
[ipv4]
method=disabled
[ipv6]
addr-gen-mode=default
method=disabled
[proxy]
Since an empty (with method=none) proxy setting is the same as no proxy setting, avoid the normalization.