Bottom line is, It's yours, Do what you want to.
But the engine is out, So it's an excellent opportunity
to treat any rust spots. And dress it up some.
If all you can do right now is a rattlecan job, Then so be it.
at least do something to encapsulate the rust. It don't have to
be pretty. You can even use a foam brush. But it will pay for
itself in the long run.
Spike