It depends on the functionality you need. Unity does a lot more than lightweight WebGL engines do.

Of course, if a lightweight WebGL engine is enough - and it might well be the case for this NASA app, which doesn't need sophisticated AI, physics, scripting, effects, etc. - then that is the better route.

There are also middle grounds between a native WebGL engine and a full native engine like Unity. There are lightweight native engines, like Cube 2,

https://developer.mozilla.org/en-US/demos/detail/bananabread

and there are even lighter than that. There isn't a dichotomy between native and compiled game engines. In fact, some native WebGL game engines use compiled portions, like PlayCanvas which uses ammo.js, a compiled native physics engine,

https://github.com/playcanvas/engine