@
Mara Jade's Father -- Yep, I know. Everything is conjecture, with varying amounts of "weight". The
Atlantis version came first, from FASA, in their Star Trek IV Update supplement, in 1986. At the time, they were considered official sources of information, being as they held license from Paramount and everything they published had to be vetted and approved. The
Ti-Ho came next, in 1987. I know Shane. He'd been working on Mr. Scott's Guide in his spare time, pretty much since TMP came out. He and Andy Probert had a somewhat fricative relationship. Shane noticed all the things wrong with the refit design*, and kept poking Andy about them, even after Andy had pointed out that those all preceded his involvement, he'd noticed them, too, and he wasn't allowed to fix them. There are many things that I like about Shane's work, and many things that just don't fit. He hadn't known about the
Atlantis when he determined that Starfleet couldn't have built a new ship so quickly, so he used the name of a ship a friend of his who was dying of cancer had come up with as a tribute.
[*
That corridor leading into Engineering would stick out into space, the torpedo bay wouldn't fit in the space allowed, the rec deck was never properly reconfigured to account for its move from centerline just below and aft of the bridge superstructure to the saucer rim (those two turboshafts were supposed to be the ones coming down from the bridge, but in the final location they come from nowhere and go to nowhere), and the fact that the turbolift cars themselves couldn't physically fit in the horizontal shafts...]
The other big fandom publication of the time, Ships of the Star Fleet, published in 1988, had the new
Enterprise as a newbuild. The author's contributions over the years carry a lot of weight in fan circles, so even though it isn't official, a nonzero portion of the fanbase swears by it.
The first mention of the
Yorktown being a contender is in 1994 in that ship's entry in the Encyclopedia. Same reason -- The Powers That Be recognized there hadn't been enough time to build a new ship. The
Yorktown was mentioned but not seen both about halfway through the FYM and in TVH. There was no supplemental information, beyond behind-the-scenes info of production intention, that it was
Constitution class of any configuration. Gene was the one who decided it would be appropriate for it to be the new
Enterprise as
Yorktown had been the original name for the hero ship in early treatments. Given that the people who were responsible for making such decisions for the production tended to go with what Gene said as gospel, that's the official unofficial fact now, unless and until something specifically overwrites it.
And it is supported by the later canon. At the end of TVH, it's back in dock and freshly repaired after its encounter with the Whalesong Probe. "Let's see what she's got," from Kirk. But there were problems. Scotty's line does refer to her as a new ship, but there's a track record for that. Decker referring to the refit original as an "almost totally new
Enterprise". Morrow referred to her as being "twenty years old" when she was actually forty, suggesting an at-least-equally extensive refit around the time Kirk took command, and potentially indicating estimates of a ship's age date more from keel-up rebuilds than original construction. If, after TMP, more
Constitution-class ships got refitted to or past the
Enterprise's specs, the
Yorktown might have had the bad luck to have been out on its first shakedown when the Probe came along, prompting immediate repairs to untested systems. Further evidence of this being the intention of the creative team is where she is to be decommissioned in 2293, at the end of TUC -- only about six and a half years after being launched under her new name. In-universe, the
Enterprise-B was launched only three months later, suggesting she was already under construction at the time, and the
Enterprise-A was only ever intended to be a placeholder for a few years until Kirk retired.
There's a bunch of additional behind-the-scenes and ancillary material to support this. From the Fact Files and his Encyclopedias through Mike Okuda, from FASA in their TNG Officer's Manual, from "Flashback" where Tuvok's parents are mentioned contemporaneously... There was a new
Excelsior-class
Yorktown in service by 2293, registry NCC-2033. Going by precedent both in-universe and real-world, it was probably already under construction when Starfleet decided to decommission the
Constitution-class ship and put
it into semi-retirement under a new name.
So what I originally posted was the non-tl;dr summation of all of this.
This is what happens when I
don't write out a full essay to give context and reasoning...
--Jonah