they are actually using different interfaces and dependencies. Checkpointing uses Flink FileSystem and the shaded Hadoop Filesystem is a special implementation of this based on the Hadoop S3 FileSystem that has all dependencies bundled in. The BucketingSink uses HDFS/Hadoop FileSystem, therefore this needs to have the correct dependency setup.
Flink 1.6. released the new StreamingFileSink which is a replacement for BucketingSink. With Flink 1.7 this will also support the bundled S3 file systems.