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Can you somehow add custom root CAs to auto provisioned JVMs? Or do I need to write my own toolchain resolver plugin to get the installed jvm paths?

if you already have custom JDKs with modified root certs, you can force Gradle to "discover" them <https://docs.gradle.org/current/userguide/toolchains.html#sec:custom_loc|https://docs.gradle.org/current/userguide/toolchains.html#sec:custom_loc>

you could also write a plugin that provisions custom JDKs, <https://docs.gradle.org/current/userguide/toolchain_plugins.html|https://docs.gradle.org/current/userguide/toolchain_plugins.html>

custom-certs.init.gradle.kts.kt

I've previously used an init script to locally inject certs into Gradle's JVM without having to modify the JDK installation, it's a hack but it does run early enough

that's not gonna help with provisioned toolchains but if they're running your own code then you just need to similarly add your own certs at runtime instead of using the system keystore