For the purpose of matching, stories which rely on knowledge of both Lord of the Rings and the Silmarillion would be considered crossovers and thus ineligible. The reason for this is because you could potentially be matched with a remixer who offered to remix Lord of the Rings but has never read and is not familiar with the Silmarillion (or vice versa), which could make remixing one of your stories very difficult for them.

That said, if you are eligible in both fandoms, and happened to be matched with someone who is familiar with both of them, they could potentially remix one of those "crossover" stories.

This was brought up in comments last year as well, so just to clarify - our eligibility restrictions on fandoms you can request to be remixed are there simply to facilitate matching. Once you've been matched with someone, you have free rein to remix any of their stories except their safe story and their previous remixes, regardless of whether the story you choose is from your matched fandom.