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Ok, thank you it helps me to understand what happened:

There was effectively a conflict between my system opencv version (3.2) and the sources (4.3.0) I wanted to build. I just set the CMAKE_IGNORE_PATH variable correctly to avoid this conflict, so rebuild OpenCV in my catkin_isolated_ws with:

catkin_make_isolated -DWITH_OPENCL=ON -DWITH_V4L=ON -DCMAKE_IGNORE_PATH=/usr/lib/x86_64-linux-gnu;/usr/include -DOPENCV_EXTRA_MODULES_PATH=../../../src/OpenCV/opencv_contrib/modules -DBUILD_EXAMPLES=ON --pkg OpenCV --install

Note: If someone is interested to use recent OpenCV version with ROS, you can find bellow step-by-step procedure to achieve it (this is the procedure I used to use OpenCV 4.3.0 with ros melodic which normally depends on OpenCV 3.2. Note that ROS packages installed via apt-get still depend on OpenCV 3.2. OpenCV 4.3.0 is used only for custom package build in the catkin_ws):

Create a catkin_isolated_ws:
check no ros env is sourced
```
env | grep PATH
```

create isolated workspace and clone sources:

mkdir -p  ~/catkin_isolated_ws/src
cd ~/catkin_isolated_ws/src
git clone https://github.com/opencv/opencv.git --branch 4.3.0 OpenCV
cd OpenCV
git clone https://github.com/opencv/opencv_contrib.git --branch 4.3.0 opencv_contrib

create a package.xml with the following content:

<package>
    <name>OpenCV</name>
    <version>4.3.0</version>
    <description>Open CV library for catkin</description>
    <maintainer email="your-email">your-name</maintainer>
    <license>your-licence</license>
    <buildtool_depend>cmake</buildtool_depend>
    <run_depend>catkin</run_depend>
    <export>
      <build_type>cmake</build_type>
    </export>
</package>

Source ROS and init workspace:

source /opt/ros/melodic/setup.bash
catkin_init_workspace

build and add the eventual opencv system's version to the cmake ignore path (CMAKE_IGNORE_PATH) (to avoid conflict with xfeatures2d):

cd ~/catkin_isolated_ws/
catkin_make_isolated -DWITH_OPENCL=ON -DWITH_V4L=ON -DCMAKE_IGNORE_PATH=/usr/lib/x86_64-linux-gnu;/usr/include -DOPENCV_EXTRA_MODULES_PATH=../../../src/OpenCV/opencv_contrib/modules -DBUILD_EXAMPLES=ON --pkg OpenCV --install

Create a catkin_ws layer for packages we want to depend on OpenCV 4.3.0:

mkdir -p  ~/catkin_ws/src
cd ~/catkin_ws/src
source ~/catkin_isolated_ws/install_isolated/setup.bash
catkin_init_workspace
cd ~/catkin_ws
catkin_make
source ~/catkin_ws/devel/setup.bash

Now we can build ROS packages depending on OpenCV, the first found version will be the one of catkin_isolated_ws which hides the /opt/ros/melodic one which also hides the OpenCV system's version (3.2 for me)

Note: You may have conflicts with ROS package cv_bridge, as it is linked against ros's opencv version (OpenCV 3.2), so you can:

build in the catkin_ws your own cv_bridge from sources which will then be build against OpenCV 4.3.0 (to hide native ros cv_bridge package linked to 3.2)
or convert ROS sensor_msgs::Image by your own to openCV format