Heiner Goebbels would be the most obvious one, Olli Virtaperko is another who's very clear (you can hear some of their music in the context of Zappa and Bach on this concert:
https://youtu.be/YpL7ELrOZrI).
imo amongst the most important composers of this generation there's a strong Zappa influence that comes through maybe just simply through inspiration but also through attitude. John Luther Adams, of the previous generation, is an incredible composer (certainly the most important American composer of recent times), who cites Zappa as having gotten him into Varese, Feldman as a teenager...but who's music sounds nothing like Frank's. Marie Incontrera I know has mentioned Zappa often (she runs the Eco-music big band, who has made some astonishing recordings)...and then I'd say FlyLo knows his way around a Zappa sound, same with Thundercat etc (but now I'm pandering, tch...)