Native dependencies usually mean you’ll need docker. Spark pre-dates docker, and just relatively recently added the Kubernetes runner, which makes dockerized jobs easy. But historically it hasn’t been easy to run a job in a containerized environment with the native dependencies you need. You can ship native deps with your job, but that’s not easy, especially if you need a rebuild with each job.
The main advantage of Spark is flexibility and interoperability. You save time by not having to write something optimized on day 1 (for something you might throw away). And you get SQL support, something Beam / Hadoop don’t have (certainly not for Python). There are lots of benchmarks where Spark SQL is not a winner, but the point is Spark will help you save development time.