Remove permitUnusedDeclared lines from build.gradle files

BEAM-11732 points towards runtimeOnly dependencies not working as expected.

As a result of BEAM-11732 not being caught by PR checks/tests, it was decided that when working on BEAM-10961, we'd add permitUnusedDeclared lines whenever an unusedDeclared error was encountered by gradlew analyzeDependencies instead of replacing a "compile" line with a "runtimeOnly" line.

Each time permitUnusedDeclared is used for the reason above, we should mark that line with a reference to this issue.

Imported from Jira [BEAM-11761](https://issues.apache.org/jira/browse/BEAM-11761). Original Jira may contain additional context.
Reported by: shehzaadn.