I’m not sure how much of this is possible without Display Suite, but here’s the setup I’ve used to index specific fields within a field collection as part of the parent entity. I use the “Search index” view mode to specify which fields I want to index on each content type. Here’s what that looks like:
As you can see, the “Versions” field and the “Associated people / organizations” field are field collections. In this example I only wanted to index a couple of fields from the “Versions” field collection as part of the search index for each “Book” node.