[Task]: Improve bundle strategy for direct runner

### What needs to happen?

It is found in some cases, elements incoming for Java direct runner are not bundled, i.e., all in bundle size = 1. Some flakiness in our unit test is likely due to this issue. For example, it is found that BigQueryWriterTest is flaky due to intermittent time out (context #25207) the issue is traced down to fact that some batch load and file load tests concurrently write thousand of files locally.

e.g. https://ci-beam.apache.org/job/beam_PreCommit_Java_GCP_IO_Direct_Phrase/57/testReport/junit/org.apache.beam.sdk.io.gcp.bigquery/BigQueryIOWriteTest/testWriteDynamicDestinationsBatchWithSchemas_0_/

the complete log will show (tested locally) 2,000 lines of org.apache.beam.sdk.io.gcp.bigquery.BigQueryRowWriter log. Since the largest concurrent file open is limited, test sometimes get stuck

### Issue Priority

Priority: 3 (nice-to-have improvement)

### Issue Components

- [ ] Component: Python SDK
- [x] Component: Java SDK
- [ ] Component: Go SDK
- [ ] Component: Typescript SDK
- [ ] Component: IO connector
- [ ] Component: Beam examples
- [ ] Component: Beam playground
- [ ] Component: Beam katas
- [ ] Component: Website
- [ ] Component: Spark Runner
- [ ] Component: Flink Runner
- [ ] Component: Samza Runner
- [ ] Component: Twister2 Runner
- [ ] Component: Hazelcast Jet Runner
- [ ] Component: Google Cloud Dataflow Runner