I remember glancing at that New Adventures of Superboy story in a quarter bin about 20 years ago. I think they were running a series called "First Times" or something like that. No doubt lots of good ideas along those lines that have never been explored. But I don't know which is the neater thing about that "comes out of warp under a red sun" story: Is it that, against astronomically long odds, he came out just close enough to a planet to glide(?) there, or that the story taught us that a human could fall out of planetary orbit and land safely on said planet using only the braking action of a cape? NASA obviously must be trying to do this stuff the hard way.
Yeah, think it was called "Strange Adventures for the first time", a series of backup stories showing Superboy's first experiences at certain things---stories included IIRC were: why Superboy put a secret cape pouch in his costume; the origin of his signal-lamp (in a tale with yet another JFK appearance); and the "Superboy meets JFK" story (which also served to explain why he can't be in two places at once when travelling to another time-era when he's alive).
Re: that entering the planet's atmosphere bit: my guess is he had enough of his invulnerability left to pull the stunt off, with the invulnerability vanishing entirely by the time he 's re-entered the atmosphere/splashed down.