Noob question: Why patch accepted by git not accepted by libgit2/pygit2?

Hi:

this is my raw diff:

diff --git a/llvm/cmake/modules/FindZ3.cmake b/llvm/cmake/modules/FindZ3.cmake
--- a/llvm/cmake/modules/FindZ3.cmake
+++ b/llvm/cmake/modules/FindZ3.cmake
@@ -75,7 +75,7 @@ unset(Z3_VERSION_STRING)
 
 # First, try to check it dynamically, by compiling a small program that
 # prints Z3's version
-if(Z3_INCLUDE_DIR AND Z3_LIBRARIES)
+if(Z3_INCLUDE_DIR AND Z3_LIBRARIES AND NOT CMAKE_CROSSCOMPILING)
   # We do not have the Z3 binary to query for a version. Try to use
   # a small C++ program to detect it via the Z3_get_version() API call.
   check_z3_version(${Z3_INCLUDE_DIR} ${Z3_LIBRARIES})

this is the repo/tag I'm trying to apply to: apple/llvm#swift-5.9-RELEASE

However:

git apply G5664b56043f1f6a838183e74275bfee389fea177.diff

works as intended, yet :

patch_content: str = patchPath.read_text()
patch: Diff = Diff.parse_diff(patch_content)
if (repo.applies(patch,raise_error=True)):
    repo.apply(patch)

results in:

hunk at line 75 did not apply

Reproduce the discrepancy using the provided diff against apple/llvm-project at swift-5.9-RELEASE. Compare git apply with Diff.parse_diff followed by repo.applies(..., raise_error=True) and repo.apply(...), then inspect the relevant libgit2/pygit2 patch-application behavior. Done means identifying why the hunk differs and documenting or correcting the behavior.