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Even when selecting a specific site in the query, $entry->enabled = false disabled the entry for all sites. I actually figured out why it wasn't saving (unrelated issue) but I'm still not clear on how to set the site for setEnabledForSite() In the docs it says "This can also be set to an array of site ID/site-enabled mappings" but I'm not clear on the format.
Yeah we don’t use many named transforms so that typically hasn’t been a problem in our case. We just generate them on the fly whenever the template is rendered and then the transformed assets are cached for future use.