[Gradle] Cleanup test mutes for gradle func tests (#133768)

(cherry picked from commit 4a745b5)

# Conflicts:
#	muted-tests.yml

Author: breskeby

muted-tests.yml

@@ -431,15 +431,6 @@ tests:
 - class: org.elasticsearch.packaging.test.DockerTests
   method: test010Install
   issue: https://github.com/elastic/elasticsearch/issues/131376
-- class: org.elasticsearch.gradle.internal.transport.TransportVersionValidationFuncTest
-  method: cannot change committed ids to a branch
-  issue: https://github.com/elastic/elasticsearch/issues/133133
-- class: org.elasticsearch.gradle.internal.transport.TransportVersionValidationFuncTest
-  method: definitions have primary ids which cannot change
-  issue: https://github.com/elastic/elasticsearch/issues/133234
-- class: org.elasticsearch.gradle.internal.transport.TransportVersionValidationFuncTest
-  method: latest files cannot change base id
-  issue: https://github.com/elastic/elasticsearch/issues/133231
 - class: org.elasticsearch.packaging.test.DockerTests
   method: test072RunEsAsDifferentUserAndGroup
   issue: https://github.com/elastic/elasticsearch/issues/131412
@@ -490,4 +481,4 @@ tests:
 #    issue: "https://github.com/elastic/elasticsearch/..."
 #  - class: "org.elasticsearch.xpack.esql.**"
 #    method: "test {union_types.MultiIndexIpStringStatsInline *}"
-#    issue: "https://github.com/elastic/elasticsearch/..."
+#    issue: "https://github.com/elastic/elasticsearch/..."