run_protocol and run_protocol_and_take_snapshots to be merged as possible

[SimonRastikian]

Background

Both functions run_protocol_and_take_snapshots and run_protocol seem similar in spirit but differ in their signature and some internals.
It might be cool to try to merge as much as possible or use helper functions.

User Story

No response

Acceptance Criteria

• Reduce code redundancy
• Make sure the changes do not break anything in the release processes, i.e., the functions signatures do not change.

Resources & Additional Notes

No response