[test] Fix intermittent timeouts in various functional tests

Summary:
Original PR message was "test: Fix intermittent timeout in p2p_permissions.py" but the impact is larger than this, notably rpc_net.py.

Pull request description:

The sync is based on `bytesrecv_per_msg["verack"]`. However, the bytes are counted before processing the message, so they are not sufficient to ensure the connection is fully up.

Backport of core#26854

Depends on D17530

Test Plan:

ninja check-functional

Reviewers: #bitcoin_abc, Fabien, PiRK

Reviewed By: #bitcoin_abc, Fabien, PiRK

Differential Revision: https://reviews.bitcoinabc.org/D17531