test: fix test failures in test/functional/p2p_timeouts.py

Summary:
From the PR discussion:

Fair enough as a temporary workaround.

The source of this bug is that not all time in net is using mocked time, giving those "rounding errors".

The long-term fix should be to use mocked time consistently.

This is a backport of core#23740

Test Plan: ninja check-functional

Reviewers: #bitcoin_abc, Fabien

Reviewed By: #bitcoin_abc, Fabien

Differential Revision: https://reviews.bitcoinabc.org/D17652