The biggest difference is that FLIF is an image encoder, SPIF/Multires is a container format.

So you can cram lossy 20x compression ratio JPEGs into Multires, optimized for each resolution. Or you could put a simplified SVG for low-res use, and detailed one for zoomed-in detail. Or hack it a bit and use Multires for loading the right-resolution video for your page. The format is just a container that tells the browser where to find the assets for each resolution.

FLIF is a lossless bitmap image encoder with progressive resolution enhancement.

TL;DR FLIF is PNG++, Multires is automatic srcset.