So I had to try this with apktool_2.3.4.jar. This resulted in a new APK with a curious "/res" folder..
The original is on the left and the new APK is on the right. The suffixes denoting different version numbers (-v17, -v21,etc) has gone. Which means the "/layout-v16" folder seems to have merged with the "/layout" folder.
I wouldn't be surprised if this causes a problem in installation..but I don't know if that happens with the more recent versions of apktool. So the issue might not be related to this at all.
It's worth opening the original and recompiled APK files in 7z and just visually comparing the two. There will always be some minor size differences but the same folders and files should be in both.
decompiled SystemUI (and other apks) on Samsung stock Pie is a total mess and won't load correctly (v-XX folders are merged). I always have to drag-n-drop the modded files from recompiled apk to original apk in order to make the app work correctly.
Am I missing any specific option to solve the problem?