Actually you only have one launcher, but it can run in two different modes.
When run from a desktop shortcut or Paradox Launcher.exe it is in standalone mode, which is intended for users who don't want to use Steam. It needs a separate installation when run that way, which is why it does not see your Steam installation of the game. Furthermore Stellaris is no longer supported on that platform, so recent patches and DLCs cannot be used in it. You must run the game from the Steam Library PLAY button now.
When run from Steam it is in Steam-compatible mode. Your problem with the changing checksum is nothing whatsoever to do with the launcher; either you are using mods, have edited game files, or have a corrupted game installation. For the latter two cases Please do a full **clean** re-install:
- move any valued save games elsewhere, and user empire designs.txt from /Documents/Paradox Interactive/Stellaris/ if you have made any ...
Read more