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I resolved the problem. When I deployed my install space from machine A to machine B, I created a folder (let's call it base) containing some shell scripts and the /home/usera/catkin_ws/install and zipped it:

base - home - usera - catkin_ws - install - ...
     - a.sh
     - b.sh

More specifically, I created the zip file like this:

mkdir base
cp --parents -r /home/usera/catkin_ws/install/* base
cp a.sh b.sh  base
zip -r base.zip base

Unzipping base.zip on machine B led to the problem I described.

However, if I create the zip file like this:

mkdir base
mkdir -p base/home/usera/catkin_ws
cp -r /home/usera/catkin_ws/install base/home/usera/catkin_ws
cp a.sh b.sh  base
zip -r base.zip base

and unzip it on machine B, I can source the base/home/usera/catkin_ws/install/setup.bash and the created ROS_PACKAGE_PATH is correct.

It seems like the --parents flag of the cp command changed something in my deployed install space, however I have no idea what it changed and how this could even happen. Anyway, I am very happy that I was able to resolve this and maybe someone knows the reason of this.