The remaining Gradle deprecation warnings are from Android Gradle Plugin (AGP), so figuring out why AGP 8.9.x+ breaks spoofSignature, and fixing that so that AGP can be updated is the only way to resolve things for Gradle 9.0:
Declaring an 'is-' property with a Boolean type has been deprecated. Starting with Gradle 9.0, this property will be ignored by Gradle.
[...]
Add a method named 'getCrunchPngs' with the same behavior and mark the old one with @Deprecated, or change the type of 'com.android.build.gradle.internal.dsl.BuildType$AgpDecorated.isCrunchPngs' (and the setter) to 'boolean'. [...]
Add a method named 'getUseProguard' with the same behavior and mark the old one with @Deprecated, or change the type of 'com.android.build.gradle.internal.dsl.BuildType.isUseProguard' (and the setter) to 'boolean'. [...]
Add a method named 'getWearAppUnbundled' with the same behavior and mark the old one with @Deprecated, or change the type of 'com.android.build.api.variant.impl.ApplicationVariantImpl.isWearAppUnbundled' (and the setter) to 'boolean'. [...]