GOOD NEWS! After 24 hours of curing, it now works perfectly 
So given the statistical impossibility of you getting flowable silicone perfectly flat & flush … and how badly the yo-yo plays when the silicone ends up uneven and rubs the string … I think you definitely want to take everyone’s advice and recess that flowable silicone using a spoon!
And @stevejspins I don’t have a favorite silicone sticker response pad, they all seem to work fine for me, but you can get a variety pack from YYF if you want to experiment.
(The main reason I wanted to learn to do flowable is for older yo-yos with odd sized silicone repsonse areas – you’ll note that this one is a VsNYYC Skywalker so it takes a weird Hat Pad size. Another reason older yo-yos may do better with recessed flowable is because their gap tends to be narrower.)