Is there any way to configure logger at shell startup directly via system.config?

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3

You can use ERL_FLAGS environment variable to specify sys.config file to load at ERTS startup (before rebar3 starts).

Example sys.config content:

[{kernel, [
    {key, value}
]}].

Example starting rebar3 shell with it:

max-au:~$ ERL_FLAGS="-config sys.config" rebar3 shell
===> Verifying dependencies...
Erlang/OTP 26 [DEVELOPMENT] [erts-13.1.4] [source-7bc70bd590] [64-bit] [smp:16:16] [ds:16:16:10] [async-threads:1] [jit:ns]

Eshell V13.1.4 (press Ctrl+G to abort, type help(). for help)
1> application:get_env(kernel, key).
{ok,value}
2>
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