Is it possible/prudent to have the delta be a RT index?
Yes, it’s fine. I know some users do so. The possible problem though is that if a document is updated and then makes it to the RT delta index you won’t have a way to “kill” it in the main, since killlist_target is not supported for RT indexes.
If not, what is the right way to programmatically trigger the rebuilding of plain indexes, such as the delta index, from within PHP, for example?
There’s only one way to rebuild a table - via indexer, you can call it via exec() in PHP.
Consider also using just a single RT table and writing a few lines script to sync from the underlying database to Manticore. BTW we have in plans to adapt indexer to RT indexes.