As of Magento 2.3, it is no longer best practice to use the flat catalog at all.As of Magento 2.3, it is no longer best practice to use the Flat Catalog feature at all.
Detailed info and justificationThe primary justfication for this are a little thin on the ground right now (updates should be made to answers here to reflect when more info is found.) Apparently, this is specificallyrevolves around forthis official troubleshooting article that recognises ongoing performance reasonsissues. As this question is relatedThe official docs links to performancethat article. Also, the Magento 2.3/2.4 docs now show an official stance on this is relevant.
Whatever issues the Magento team have found with flat catalog must outweigh the benefits of converting EAV data to a flat structure.
Some tweets that start toare relevant, they shed some light on this change when we first discovered this change in tact from the Magento team and still now contain some interesting thoughts: