Comfortable filling, despite appearances? (4,4)
I believe the answer is:
deep down
This clue is a double definition.
'comfortable filling' is the first definition.
(feathers are soft when deep layer used as filling)
'despite appearances?' is the second definition.
(inmost feelings despite appearances to contrary)
(Other definitions for deep down that I've seen before include "despite appearances" , "Fundamentally" .)