[Task]: Improve Beam's compliance with Pyrefly checks

### What needs to happen?

[Pyrefly](https://pyrefly.org/) is being adopted as a new static type checker for many Python projects, and as a result a pyrefly.toml configuration is being added to Beam (the PR adding the file will be linked below.) A number of violations of default checks exist within Beam, and will be suppressed within this configuration file initially. An effort should be taken to reduce the number of checks we suppress in Beam, and this issue will track that work.

### Issue Priority

Priority: 3 (nice-to-have improvement)

### Issue Components

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