Hi Sriram,
according to [1], what you see is a new security "feature" in Mac 10.12. If you try to launch an app from the Downloads folder, a "Gatekeeper" moves to and launches the app from a read-only folder. The TLA+ Toolbox cannot run from a read-only folder unless the metadata area - via the -data parameter - is located in a writable location. You can either pass the -data parameter (like you did) or move the TLA+ Toolbox app bundle into /Applications before launching.
Note that the upcoming TLA+ Toolbox release [2], by default
stores the metadata area in ~/.tlaplus/. Thus, it is unaffected by
the Gatekeeper even if run from Downloads.
Markus