Yup, that’s where I usually end up, unless I am fortunate enough to have something nearby to clone over it.
This picture, from my large format photography web site, had several flare spots in front of the vaguely triangular rocks in the middle ground. But when you’ve got a 300Mpx scan from a 5" x 4" negative to play with, it’s easier to be more precise. In this case, I used Photoshop to change the tonality of the flare spots to that of some neighbouring rocks.
Correct.
Certainly modern multi-coated lenses help but, if the sun is able to penetrate into the lens, it can also reflect off the inner structure of the lens as well as refract through the glass. Which is where a good rectangular compendium hood comes into the equation, where you can place the edge very precisely on the edge of the frame, observing very carefully that none of the lens interior is in direct sunlight, whilst avoiding cutting into the frame with the hood.
Believe it or not, we used such a hood on this shot but the sun was just a tad too low in the sky (possibly it had dropped whilst we were calculating the exposure and loading the film).
In short, don’t shoot into the sun 
But since contre-jour shots are so attractive, as we found with the above shot, the only way to do that is to use a decent compendium hood, or even (a lot cheaper) a French flag, and take your time to align it properly but not too long if the sun is setting as fast as it was then (sort of slow, slow, quick, quick, slow) 
