I do think it unlikely and surprising if FLI funds were simply directed into the MIRI technical research agenda.

FLI's request for proposals links to their research priorities document, which cites 4 MIRI papers and states, "Research in this area [...] could extend or critique existing approaches begun by groups such as the Machine Intelligence Research Institute [76]." (Note that [76] is MIRI's technical agenda document.)

So obviously they don't think MIRI's current research is a waste of resources or should be deprioritized. If they end up not funding any MIRI projects, I would think it probably has more to do with MIRI having enough funding from other sources than any disagreements between FLI and MIRI over research directions.