Please note that some applications do require to write their settings to registry(since they are not native portable applications). But your registry entries are handled by LiberKey tool called
LiberKeyPortabilizer as mentioned above.
So every time when you open a LiberKey application all entries are written to the registry and are backed up in the application folder and deleted from the registry when you close it.
So your registry remains
clean.
"LiberKey" makes available the applications cutomised to run as Portable Application.
Hence you are required to update using LiberKey updater only and
NOT directly from within the application.
Hope it's clear now.