For CompCert, the more worrying is the correctness of "extraction". This is somewhat technical, you should be able to search if you are curious. CakeML solves extraction problem.
For HOL, Proof Technologies Ltd developed HOL Zero, which is solely dedicated to trustworthiness without bells and whistles. Bells and whistles are absolutely necessary for proof development. The idea is to use HOL Zero at the end, after proof is finished. It's like coqchk idea on steroid. http://proof-technologies.com/holzero/
Summary: CompCert trusts coqchk and extraction. CakeML trusts HOL, hopefully something like HOL Zero can be used in the future.
1. Implementations can be wrong, so we want a formal proof system
2. The proof system can be wrong, so we want to apply the proof system to itself
3. But the proof system may be wrong (either in implementation or specification) in a way such that its self-proof is actually invalid
At some point, we want to assert some property (completeness, correctness) of the system as a whole, but whenever we augment the system to allow this, that augmented system's own properties now come into question.
Godel’s Proofs rely on statement encoding using properties of integers not required for these logic systems.
Presburger Arithmetic, for example, avoids Godel incompleteness, yet provides a decent system for a lot of work.