flask_sqlalchemy `pool_pre_ping` only working sometimes

For testing, I amend the MYSQL (RDS) parameters as follows;

wait_timeout = 40 (default was 28800)

max_allowed_packet = 1GB (max - just to be sure issue not caused by small packets)

net_read_timeout = 10

interactive_timeout unchanged

Then tested my app without pool_pre_ping options set (defaults to False), kept the app inactive for 40 seconds, tried to login, and i get

Nov 14 20:05:20 ip-172-31-33-52 gunicorn[16962]: Traceback (most recent call last):
Nov 14 20:05:20 ip-172-31-33-52 gunicorn[16962]:   File "/var/www/api_server/venv/lib/python3.6/site-packages/sqlalchemy/engine/base.py", line 1193, in _execute_context
Nov 14 20:05:20 ip-172-31-33-52 gunicorn[16962]:     context)
Nov 14 20:05:20 ip-172-31-33-52 gunicorn[16962]:   File "/var/www/api_server/venv/lib/python3.6/site-packages/sqlalchemy/engine/default.py", line 507, in do_execute
Nov 14 20:05:20 ip-172-31-33-52 gunicorn[16962]:     cursor.execute(statement, parameters)
Nov 14 20:05:20 ip-172-31-33-52 gunicorn[16962]:   File "/var/www/api_server/venv/lib/python3.6/site-packages/MySQLdb/cursors.py", line 206, in execute
Nov 14 20:05:20 ip-172-31-33-52 gunicorn[16962]:     res = self._query(query)
Nov 14 20:05:20 ip-172-31-33-52 gunicorn[16962]:   File "/var/www/api_server/venv/lib/python3.6/site-packages/MySQLdb/cursors.py", line 312, in _query
Nov 14 20:05:20 ip-172-31-33-52 gunicorn[16962]:     db.query(q)
Nov 14 20:05:20 ip-172-31-33-52 gunicorn[16962]:   File "/var/www/api_server/venv/lib/python3.6/site-packages/MySQLdb/connections.py", line 224, in query
Nov 14 20:05:20 ip-172-31-33-52 gunicorn[16962]:     _mysql.connection.query(self, query)
Nov 14 20:05:20 ip-172-31-33-52 gunicorn[16962]: MySQLdb._exceptions.OperationalError: (2013, 'Lost connection to MySQL server during query')

Added the pool_pre_ping like this (Using flask_sqlalchamy version 2.4.1);

import os
from flask import Flask
from flask_sqlalchemy import SQLAlchemy as _BaseSQLAlchemy


class SQLAlchemy(_BaseSQLAlchemy):
    def apply_pool_defaults(self, app, options):
        super(SQLAlchemy, self).apply_pool_defaults(app, options)
        options["pool_pre_ping"] = True
#        options["pool_recycle"] = 30
#        options["pool_timeout"] = 35

db = SQLAlchemy()


class DevConfig():
    SQLALCHEMY_ENGINE_OPTIONS = {'pool_recycle': 280, 'pool_timeout': 100, 'pool_pre_ping': True} # These configs doesn't get applied in engine configs :/
    DEBUG = True
    # SERVER_NAME = '127.0.0.1:5000'
    SQLALCHEMY_DATABASE_URI = os.getenv('SQLALCHEMY_DATABASE_URI_DEV')
    SQLALCHEMY_TRACK_MODIFICATIONS = False

config = dict(
    dev=DevConfig,
)

app = Flask(__name__, instance_relative_config=True)
app.config.from_object(config['dev'])

# INIT DATABASE
db.init_app(app)
with app.app_context():
    db.create_all()

-----------run.py
app.run(host='127.0.0.1', port=5000)

With this, now the webapp manages to get new connection even after MySQL server has closed the previous connection. It always works fine when I access the database right after its closed by server (tried max 50 seconds after)... but when I keep connection inactive for long time (haven't noted, but ~ >10-15 min), again I see same error.
According to the docs, (especially the section Dealing with disconnects), the pool_pre_ping option should handle this kind of scenario at background rite? Or is there any other timeout variable that I need to change in MySQL server?

from flask_sqlalchemy `pool_pre_ping` only working sometimes