Just to answer my own question and maybe to help some Linux users. I gave UE4 on Linux another try and have looked more into the Unreal Build Tool and have played around with parameters. You can define a randomly named module as a parameter and then hot reload works fine. Especially the -ModuleWithSuffix parameter is necessary for a proper hot reload functionality.
I have written a bash script ue4build that looks like
#!/bin/bash
UNREAL_PATH=[PATH_TO_YOUR]/UnrealEngine;
RANDNUM=$(( ( RANDOM % 1000 ) + 1000 ));
CURR_DIR=`pwd`;
PROJ_NAME=$(basename ${1%.uproject});
PROJ_NAME_MODULE="${PROJ_NAME},${RANDNUM}";
${UNREAL_PATH}/Engine/Build/BatchFiles/Linux/RunMono.sh ${UNREAL_PATH}/Engine/Binaries/DotNET/UnrealBuildTool.exe -ModuleWithSuffix=$PROJ_NAME_MODULE Linux Development -TargetType=Editor -Project="${CURR_DIR}/${PROJ_NAME}.uproject" -canskiplink "${CURR_DIR}/${PROJ_NAME}.uproject" -progress
Put the script in one of your executable directories and make it executable with chmod u+x. Then you can build your project with hot reload just by using the following command
ue4build PATH_TO/YOUR_UE4_PROJECT.uproject