Obstruction or not

You have nothing, ie no obstruction. As long as the fielder did not totally block access to the base, no obstruction.
And, on your second comment, not totally true, a fielder can set up in the base path, the runner possibly might be able to slide under the fielder?
HTBT.

so can a catcher set up 10 ft up the line between home and 3rd?

OBR 2.0 Definition of Obstruction...an act by the fielder who, while not in pocession of the ball and not in the act of fielding the ball, impedes the progress of a runner.

So if your catcher is fielding an off line throw it's OK. the runner may leave the baseline to avoid contact If he's out there just gumming things up ..Obstruction.

So back to the original question about the play at 2nd as long as the fielder is making a legimate play it's generally going to be nothing. He can set up straddling the bag as long as the runner has a place to go it's nothing.

This is rally not a lot different than a play at 1st where the throw is on the home plate side of first and the 1st baseman comes of the bag to catch and tag rather than hold the bag for the Put out. Of course on that play if the runner is out of the lane he can be called for interference.