build.ninja is missing dependencies present in cmake subproject

Describe the bug
I have a cmake project that I can build with cmake+ninja using cmake -G Ninja -S src -B build; ninja -C build that I cannot build from meson with a simple wrapper. The meson generated build.ninja is missing dependencies that are present in the cmake genearted build.ninja, which seems to be the cause of the meson compile failure.

The missing dependencies are for generated header files and are defined in CMake with set_source_files_properties().

To Reproduce
Create sample meson project:

mkdir -p project/subprojects

cat > project/meson.build << 'EOF'
project('experiment', ['c'], version: '1.0.0', meson_version: '>=0.58.0', )
cmake = import('cmake')
uncrustify_options = cmake.subproject_options()
uncrustify_options.add_cmake_defines({ 'NoGitVersionString': true })
uncrustify_proj = cmake.subproject('uncrustify', options: uncrustify_options)
EOF

cat > project/subprojects/uncrustify.wrap << 'EOF'
[wrap-git]
url = https://github.com/alex-tomlinson/uncrustify.git
revision = alex-fix-deps-01
EOF

Building with meson fails:

meson setup project build1
ninja -C build1

Error output:

../project/subprojects/uncrustify/src/punctuators.cpp:34:10: fatal error: punctuator_table.h: No such file or directory
   34 | #include "punctuator_table.h"

Building with cmake is successful:

cmake -G Ninja -S project/subprojects/uncrustify -B build2
ninja -C build2

Compare entry for punctuator.cpp.o in each build.ninja file. Note punctuator_table.h and some others are missing from meson's build.ninja file.

$ grep '^build.*punctuators.*o:' build1/build.ninja  build2/build.ninja 
build1/build.ninja:build subprojects/uncrustify/cm_uncrustify.p/src_punctuators.cpp.o: cpp_COMPILER ../project/subprojects/uncrustify/src/punctuators.cpp || subprojects/uncrustify/option_enum.h
build2/build.ninja:build CMakeFiles/uncrustify.dir/src/punctuators.cpp.o: CXX_COMPILER__uncrustify_ /home/atomlinson/xxmeson/project/subprojects/uncrustify/src/punctuators.cpp | token_names.h uncrustify_version.h src/option_enum.h src/punctuator_table.h || cmake_object_order_depends_target_uncrustify

Expected behavior
Expect meson setup/compile to succeed.

system parameters

• Is this a cross build or just a plain native build (for the same computer)?
  native
• what operating system (e.g. MacOS Catalina, Windows 10, CentOS 8.0, Ubuntu 18.04, etc.)
  Fedora 34
• what Python version are you using e.g. 3.8.0
  Python 3.9.2
• what meson --version
  0.58.2
• what ninja --version if it's a Ninja build
  1.10.0.git.kitware.jobserver-1
• Other
  cmake version 3.19.7

Reproduce the failure with the provided Meson wrapper and compare the generated build1/build.ninja entry for punctuators.cpp.o with the CMake-generated build2/build.ninja entry. Start by tracing Meson's cmake.subproject() handling of CMake set_source_files_properties() dependencies. Done means Meson-generated Ninja dependencies include the generated headers and the native setup/compile succeeds.