yes, we (in the mod world) use CSK fillers (both ones we make from Cherry rivets and the ClickBond pre-formed ones) and I know some OEMs use them.
Using them in a double flush instance such as yours would be "odd" ... not Wrong, just unusual. "enough thickness" ... well that would depend on the fatigue environment but I'd apply the typical "2/3rd thickness" rule as applying to the total CSK depth (ie the sum of the CSK depths < 1/3 thickness).
But this is one person's opinion ... you need to talk to whoever is approving your work (the delegate).
Where are you ? (US, Europe, Africa, China, ...)
What type of plane ? (commercial, freight, ...)
If commercial, you may need to ask the OEM.
"Hoffen wir mal, dass alles gut geht !"
General Paulus, Nov 1942, outside Stalingrad after the launch of Operation Uranus.