Hello!
It appears that when building using cargo-apk 0.9.3 and later the RUSTFLAGS set in /.cargo/config.toml are not being included. In our code-base we depend on the flag rust flag "--cfg tokio_unstable" being set. However when building this flag is not being set. Earlier version of cargo-apk like 0.9.2 does not show this behavior.
Quickly skimming the diff there appears to have been some changes to how flags are being handled, though I haven't looked to close yet.