Do you have a cli.ini in /etc/letsencrypt that specifies must-staple?
Because it does sound strange that Certbot would restore that setting even if removed from the renewal profile. I am not sure False works but when not used nothing appears in the renewal profile.
Also note your Apache is not stapling today. Your cert says must-staple, but, your Apache just isn't doing it. And, browsers tend not to care so you may not have noticed it.
See: SSL Server Test: www.rrm.me.uk (Powered by Qualys SSL Labs)