Thanks for the question. A quick test against a staging copy of a WooCommerce store shows no problems. But I am not planning to add testing this compatibility to my suite of tests.
This Meta Optimizer plugin takes a different approach to handling the key/value tables (postmeta, usermeta, and termmeta) than mine does. Mine adds keys that match the shapes of many queries in WordPress, and does not require altering the queries before running them. That is a good choice for database optimization because it does not require testing query edge cases.
This one creates denormalized versions of the key/value tables containing some of the keys. That’s a good idea too: the key-value store approach is notoriously ineffecient. If it were possible to refactor the guts of WordPress and its plugin / theme ecosystem to move many common values to a denormalized table, it would be great.