No problem, If you do a backup with anonymised, if you use it to restore your site, the data will be restored in the anonymised format.
Anonymised data is only really suitable for when you are testing with something like a clone.
For example, you are having issues with UpdraftPlus on your site, I ask you if we can do a clone for testing. I would need clone the DB (for the plugin settings) but I would use this feature so that I don’t copy your customer data over (I don’t need it so it’s best not to have it). It’s great for GDPR compliance.
However if your site went down and you started with a blank WP install, when you restored the data you would not have your customer data (which would be fairly useless on an e-commerce site).