I could swear I've seen you say this. Maybe I'm mis-remembering? ISTR it was that for each table source in a query SQLite3 uses just one index (or the table itself) for indexing or scanning to find relevant rows in that table source.
SQLite tries to only uses indexes in situations where they help the query run faster. SQLite is not limited in its use of indexes. It is just that the use of multiple indexes for a single FROM-clause term is rarely helpful.