net-dns/knot-1.6.4 was released on June 16. The ebuild works if you rename 1.6.3 to 1.6.4, but the Makefile patch requires a slight change. Reproducible: Always
Created attachment 406064 [details, diff] 1.6.4-dont-create-extra-directories.patch
Version updated to 1.6.6. Thanks for the bug and patch.