CMake: link against two precompiled libraries dependent on different versions of third library

I'm trying to compile a project where I'm linking against precompiled versions of two libraries (PCL and Matlab), that are compiled against different versions of Boost (1.58 and 1.56).

This gives me many warnings when I build my project:

Cannot generate a safe runtime search path for target Test because 
files in some directories may conflict with libraries in implicit directories:

runtime library [libpng12.so.0] in /usr/lib/x86_64-linux-gnu may be hidden 
by files in:
  /usr/local/MATLAB/R2017b/bin/glnxa64

and so on for other libraries (libtiff, libfreetype, libexpat, libxml2, libQt5OpenGL...), but none for boost.

When I compile and run my program I get this error

*** Error in `/home/user/Test': free(): invalid pointer: 0x0000000000bf36a8 ***
======= Backtrace: =========
/lib/x86_64-linux-gnu/libc.so.6(+0x777e5)[0x7f9cf1c507e5]
/lib/x86_64-linux-gnu/libc.so.6(+0x8037a)[0x7f9cf1c5937a]
/lib/x86_64-linux-gnu/libc.so.6(cfree+0x4c)[0x7f9cf1c5d53c]
/lib/x86_64-linux-gnu/libc.so.6(__cxa_finalize+0x9a)[0x7f9cf1c1336a]
/usr/local/MATLAB/R2017b/bin/glnxa64/libboost_filesystem.so.1.56.0(+0x7646)[0x7f9ce9eda646]

I suspect it is because it adds all the libraries to the same search path and links PCL to Matlab's version of Boost which gives the error and warnings. I have spent a lot of time trying to get it to link without crashing, but to no avail.

Inspired by: link path confusion after target_link_libraries call I tried adding Matlab using add_library,

add_library(eng STATIC IMPORTED)
set_property(TARGET eng PROPERTY IMPORTED_LOCATION ${Matlab_ENG_LIBRARY})
set_property(TARGET eng PROPERTY INTERFACE_INCLUDE_DIRECTORIES /usr/local/MATLAB/R2017b/bin/glnxa64/)
target_link_libraries(${PROJECT_NAME} eng)

(and many variations of this) but I've been unable to find a combination that solved the problem, as I also run into the same problems as the asker.

It seems that another question is about a very similar problem, but it has not been answered MATLAB Libraries conflict with Existing Libraries - CMake Crash

I think I could solve the problem by compiling PCL and boost 1.56 from scratch, but I would like to avoid that.

Minimal "working" example:

CMakeLists.txt

project(Test)
cmake_minimum_required(VERSION 2.8)
add_executable(${PROJECT_NAME} main.cpp)

#PCL
find_package(PCL 1.3 REQUIRED COMPONENTS)
include_directories(${PCL_INCLUDE_DIRS})
target_link_libraries(${PROJECT_NAME} ${PCL_LIBRARIES})

#Matlab
find_package(Matlab REQUIRED ENG_LIBRARY)
include_directories(${Matlab_INCLUDE_DIRS})
target_link_libraries(${PROJECT_NAME} ${Matlab_ENG_LIBRARY})

main.cpp

#include <pcl/io/ply_io.h>
#include "engine.h"

int main() {
    pcl::PLYReader ply_reader;
    return 0;
}

void not_called_function() {
    Engine *ep;
    ep = engOpen("");
    return;
}

Anything that can help me on the way to a solution will be greatly appreciated.