I have got into a massive muddle with my certificates and certbot and I would really like to start again. I have seen another question similar to this but, instead of answering it, a long winded discussion about how to resolve the mess ensued.
Is it possible to remove all the changes made by certbot from my server with one or at least a small number of commands?
I am not sure. I don't know what your vantage point is in defining a small number.
I know I build and rebuild systems until it is what I want, so often I restart as my step 1.
For most people I believe that is not desirable.
If you have a mess there is not likely a single command that will fix it. Unless you have a backup from before that you can restore from.
These steps relate to your config as described in your earlier thread (no one else should rely on this). You say you want to remove all changes and it looks like certbot created your HTTPS VirtualHosts. If that's the case you could try:
Editing each HTTP site (port 80) and remove any redirects to HTTPS
Run a2dissite for each of your HTTPS sites (those with *-le-ssl.conf files)
Delete the -le-ssl.conf files from the /sites-available/ folder
If you made manual changes to the -le-ssl.conf files then makes notes or backups of those changes to re-apply later.
If you still plan to use certbot I would delete all the certs shown by certbot certificates. You say they are a mess so no sense keeping them. If you've done the above and restarted Apache you won't have any functioning HTTPS domains so it is safe to delete the certs. You might want to review this topic on Deleting Certs before proceeding
That all said, I can't test this on your config obviously. So, rely on your own admin skills to adjust as needed. Take backups and good notes as you proceed in case something goes awry.
Lastly, if you want full control of your web server config you should use the --webroot method instead of the apache plug-in. Webroot will only obtain certs and leave you to install them in your webserver (that is, make all the required config changes).