Limited evidence doesn't mean it doesn't work.

The reasoning behind flossing makes a lot of sense:

1. You remove food sources for streptococcus mutans

2. You avoid inflammation from teeth shifting

3. You disrupt biofilm (plaque) formation in the joints of your teeth

I imagine the evidence is limited because genetics, diet and other oral hygiene routines significantly impact the outcome. There is a whole microflora system in your mouth, and the advice is to throw everything (floss, scrape tongue, mouthwash, brush) at it for everyone because personalising it is not worth the effort.