Shell: fix Distributed_db_message.Bounded_encoding.set_*

Context

Distributed_db_message.Bounded_encoding.set_* functions are supposed to affect the encoding of Distributed_db_message.t.

It was sadly not working for set_mempool_max_operations and set_protocol_max_size. The previous implementation also made it hard to check whether other set_* function were correct.

The MR rewrites the logic to make the correctness much more obvious.

Manually testing the MR

Checklist

• Document the interface of any function added or modified (see the coding guidelines)
• Document any change to the user interface, including configuration parameters (see node configuration)
• Provide automatic testing (see the testing guide).
• For new features and bug fixes, add an item in the appropriate changelog (docs/protocols/alpha.rst for the protocol and the environment, CHANGES.rst at the root of the repository for everything else).
• Select suitable reviewers using the Reviewers field below.
• Select as Assignee the next person who should take action on that MR