diff --git a/src/cargo/core/compiler/build_runner/compilation_files.rs b/src/cargo/core/compiler/build_runner/compilation_files.rs
index cad6f0db7731..ea86eb64be34 100644
--- a/src/cargo/core/compiler/build_runner/compilation_files.rs
+++ b/src/cargo/core/compiler/build_runner/compilation_files.rs
@@ -649,6 +649,23 @@ fn compute_metadata(
     // with user dependencies.
     unit.is_std.hash(&mut hasher);
 
+    // While we don't hash RUSTFLAGS because it may contain absolute paths that
+    // hurts reproducibility, we track whether a unit's RUSTFLAGS is from host
+    // config, so that we can generate a different metadata hash for runtime
+    // and compile-time units.
+    // This is essentially a hack for fixing rust-lang/cargo#14253.
+    if unit.kind.is_host() && !bcx.gctx.target_applies_to_host().unwrap_or_default() {
+        let host_info = bcx.target_data.info(CompileKind::Host);
+        let target_configs_are_different = unit.rustflags != host_info.rustflags
+            || unit.rustdocflags != host_info.rustdocflags
+            || bcx
+                .target_data
+                .target_config(CompileKind::Host)
+                .links_overrides
+                != unit.links_overrides;
+        target_configs_are_different.hash(&mut hasher);
+    }
+
     MetaInfo {
         meta_hash: Metadata(hasher.finish()),
         use_extra_filename: should_use_metadata(bcx, unit),
diff --git a/tests/testsuite/rustflags.rs b/tests/testsuite/rustflags.rs
index 245aa499232d..ec612c4ef061 100644
--- a/tests/testsuite/rustflags.rs
+++ b/tests/testsuite/rustflags.rs
@@ -1691,24 +1691,14 @@ fn host_config_shared_build_dep() {
 [LOCKING] 2 packages to latest compatible versions
 [DOWNLOADING] crates ...
 [DOWNLOADED] cc v1.0.0 (registry `dummy-registry`)
-[WARNING] output filename collision.
-The lib target `cc` in package `cc v1.0.0` has the same output filename as the lib target `cc` in package `cc v1.0.0`.
-Colliding filename is: [ROOT]/foo/target/debug/deps/libcc-[HASH].rlib
-The targets should have unique names.
-Consider changing their names to be unique or compiling them separately.
-This may become a hard error in the future; see <https://github.com/rust-lang/cargo/issues/6313>.
-[WARNING] output filename collision.
-The lib target `cc` in package `cc v1.0.0` has the same output filename as the lib target `cc` in package `cc v1.0.0`.
-Colliding filename is: [ROOT]/foo/target/debug/deps/libcc-[HASH].rmeta
-The targets should have unique names.
-Consider changing their names to be unique or compiling them separately.
-This may become a hard error in the future; see <https://github.com/rust-lang/cargo/issues/6313>.
 [COMPILING] cc v1.0.0
 [RUNNING] `rustc [..]--cfg from_host[..]`
 [RUNNING] `rustc [..]--cfg from_target[..]`
-[ERROR] failed to build archive: No such file or directory                                                                                                               │
-
-[ERROR] could not compile `cc` (lib) due to 1 previous error
+[COMPILING] bootstrap v0.0.0 ([ROOT]/foo)
+[RUNNING] `rustc --crate-name build_script_build [..]--cfg from_host[..]`
+[RUNNING] `[ROOT]/foo/target/debug/build/bootstrap-[HASH]/build-script-build`
+[RUNNING] `rustc --crate-name bootstrap[..]--cfg from_target[..]`
+[FINISHED] `dev` profile [unoptimized] target(s) in [ELAPSED]s
 
 "#]])
         .run();