Anyway to set proxy via flag or in the config file? Or make rclone read env variables from the config file?

welcome to the forum,

not that i know of, as rclone relies on the OS.

have you seen this topic?
https://forum.rclone.org/t/add-proxy-to-rclone/41731

what about something like
export http_proxy=http://proxyserver:12345 && rclone sync...