Validate representative PyBNF examples against the BNGsim default path

[wshlavacek]

Context

Targeted unit tests are necessary but not sufficient for changing PyBNF's
default simulator path. Representative examples should be validated against the
BNGsim-backed path to catch integration issues in realistic workflows.

Task

Validate representative PyBNF examples against the BNGsim default path.

Acceptance Criteria

• Select representative BNGL deterministic, BNGL stochastic, and NF examples.
• Run the selected examples through the BNGsim-backed path.
• Verify output columns, observables, objective scoring, stochastic behavior,
  and generated files where applicable.
• Compare against legacy behavior using tolerances appropriate for deterministic
  and stochastic methods.
• Add regression tests or documented validation scripts for examples that catch
  integration bugs.
• Document any examples that cannot yet run through BNGsim and the reason.