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What does it mean to “build a subproject on its own”? Is there a minimum reproducer available? the version catalog is semantically equivalent to directly specifying the version - no differences there.

pluginManagement { plugin { ... } }

is simply longer available to define a default version for a plugin to be used in the build. Version catalogs feature (doesn't matter whether used from settings script or with TOML file to define the versions) is just a newer feature that is available now and that I personally would prefer. But either way nothing should use the "latest version in the world" unless you do something really non-standard and strange. As Chris said, you probably need to provide an MCVE to show what you mean.

Minimum reproducer: https://github.com/GlenKPeterson/gradleIssue

Not sure how your MCVE is related to your question. The error you show in the readme is because you didn't do

libs.plugins.dokka

and so on, but

libs.kotlin.dokka

.

Yes. Correcting the plugins block to the below allows the project to be successfully executed.

plugins {
    `java-library`

    alias(libs.plugins.m.versions)
    alias(libs.plugins.dokka)
    alias(libs.plugins.kotlin.jvm)
}

@Suppress("DSL_SCOPE_VIOLATION")
    alias(libs.plugins.m.versions)

Seems to suppress the IDE error.

Yes, or you just ignore it, or install the little work-around plugin mentioned in https://youtrack.jetbrains.com/issue/KTIJ-19370 🙂