How to remove c++ compilation flag of ninja from cmake run by VCPKG?

Question

I'm trying to build boost-container on Raspberry Pi 4 with VCPKG package manager. The problem is that one of compilation flags -m64 is invalid for compiler on rpi (but is OK for PCs), so I need to remove the flag. It is extremally hard, because VCPKG is using cmake, to build with ninja, which uses b2 to build boost.

I need to have version of VCPKG: ebe505081b667a9f9a56596057f63ed20be237a5. So to reproduce the problem on RPI:

git clone https://github.com/microsoft/vcpkg.git
cd vcpkg/
git checkout ebe505081b667a9f9a56596057f63ed20be237a5
./bootstrap-vcpkg.sh -useSystemBinaries # for that version it is necessairy for RPI
./vcpkg install boost-container

After running commands above above I see problem with the -m64 flag:

Starting package 17/17: boost-container:x64-linux
Building package boost-container[core]:x64-linux...
-- Downloading https://github.com/boostorg/container/archive/boost-1.71.0.tar.gz...
-- Extracting source /home/agh/vcpkg/downloads/boostorg-container-boost-1.71.0.tar.gz
-- Using source at /home/agh/vcpkg/buildtrees/boost-container/src/ost-1.71.0-aa14783b9a
-- Configuring x64-linux-dbg
-- Configuring x64-linux-rel
-- Building x64-linux-dbg
CMake Error at scripts/cmake/vcpkg_execute_build_process.cmake:136 (message):
    Command failed: /usr/bin/cmake --build . --config Debug --target install -- -v
    Working Directory: /home/agh/vcpkg/buildtrees/boost-container/x64-linux-dbg
    See logs for more information:
      /home/agh/vcpkg/buildtrees/boost-container/install-x64-linux-dbg-out.log

Call Stack (most recent call first):
  scripts/cmake/vcpkg_build_cmake.cmake:91 (vcpkg_execute_build_process)
  scripts/cmake/vcpkg_install_cmake.cmake:24 (vcpkg_build_cmake)
  installed/x64-linux/share/boost-build/boost-modular-build.cmake:90 (vcpkg_install_cmake)
  ports/boost-container/portfile.cmake:14 (boost_modular_build)
  scripts/ports.cmake:94 (include)


Error: Building package boost-container:x64-linux failed with: BUILD_FAILED
Please ensure you're using the latest portfiles with `.\vcpkg update`, then
submit an issue at https://github.com/Microsoft/vcpkg/issues including:
  Package: boost-container:x64-linux
  Vcpkg version: 2019.09.12-unknownhash

Additionally, attach any relevant sections from the log files above.

But the problem was:
gcc.compile.c /home/agh/vcpkg/buildtrees/boost-container/x64-linux-dbg/boost/build/e3cde813a01d557174a1b469417f2150/alloc_lib.o
c++: error: unrecognized command-line option ‘-m64’

    "/usr/bin/c++" -x c -m64 -pthread -O0 -fno-inline -Wall -g  -DBOOST_ALL_NO_LIB=1 -DBOOST_CONTAINER_STATIC_LINK=1  -I"../include" -I"/home/agh/vcpkg/installed/x64-linux/include" -c -o "/home/agh/vcpkg/buildtrees/boost-container/x64-linux-dbg/boost/build/e3cde813a01d557174a1b469417f2150/alloc_lib.o" "../src/alloc_lib.c"

...failed gcc.compile.c /home/agh/vcpkg/buildtrees/boost-container/x64-linux-dbg/boost/build/e3cde813a01d557174a1b469417f2150/alloc_lib.o...
...failed updating 1 target...
...updated 5 targets...
ninja: build stopped: subcommand failed.

I've checked working directory:

find /home/agh/vcpkg/buildtrees/boost-container/x64-linux-dbg -type f | xargs grep m64

but there is nothing to remove the flag I've noticed.

The only solution I found is to create compiler wrapper binary, which ignores only that one flag -m64 - but I hope it is better solution to create patch to CMake of boost-contaier?