The Second Method sounds good... especially because configs have to be in pbos so server that dont allow third-party Mods are also semi safe from people using Extensions for bad stuff. even if i cant think of what bad stuff they could do with clientside extensions.
But... Both Methods are clientside.. And people who can tamper Extensions can also Tamper client-side pbos.
My Idea is bisigns for Dlls.. I Think that would do the Job with most of the code already there.

This get's even more Important with the rise of Intercept and it's Plugins.

#chris5790 from Arma Discord got me that Idea.
This could also solve the "Battleye master Server is down and is blocking our Extensions. So we can't use ACRE/TFAR/ACE anymore"
I get messaged a couple times per month with "Battleye blocks my TFAR". I feel like the Bisigns for Extensions could completly replace the Battleye whitelisting process. If servers allow Bisigns for Hacks. We can't do much about it anyway.

Intercept just added that yesterday. Code-signed binary and self-signed CA certificate in PBO.
Signature get's grabbed from binary and certificate from PBO (Which is protected by bisign) and if that doesn't match Intecept denies loading the Plugin.