Here is a partial answer to my own question. Assume that the atomic engines of the DY-100 class ships were a form of atomic rockets that used heat, electricity, or other energy generated by fission, fusion, or antimatter to propel water or other substances out of the nozzles for reaction.
Maybe DY-100 class ships could accelerate for months or years at a time, and then flip over halfway to the destination and decelerate for the rest of the trip. On a trip where the average speed was 10,000,000 miles per year, the top speed right before deceleration would be 20,000,000,000 miles per year. So for a one way trip to Neptune lasting half a year the ship would carry enough fuel to accelerate to 20,000,000,000 miles per hour, and an equal amount of fuel to decelerate to zero speed.
For a round trip to Neptune and back in one Earth year, the astronauts might plan to refuel with ices of water, ammonia, or methane on a moon or asteroid orbiting Neptune. But safety regulations might require DY-100 ships to carry four times the fuel needed to accelerate to about 20,000,000,000 miles per year. And thus they would have to have fuel tanks that big.
If Khan's people took along a solar sail or a magnetic drag and planned to use it to decelerate without expanding reaction mass, they could use all the reaction mass to accelerate at the start of the journey,and thus reach speeds eight times the average speed of 10,000,000,000 miles per year in a one year round trip to Neptune.
Thus the Botany Bay could accelerate to 80,000,000,000 miles per year and could reach Proxima Centauri in about 312 years.
In the last few years evidence of a planet nine has been found. It is supposed to orbit in a highly elliptical orbit about 200 to 700 Astronomical units from the Sun, and is thought to probably be near the farthest point of its orbit. So it is probably about 700 times 92,956,000 miles, or about 65,069,200,000 miles from the Sun.
If a constantly accelerating ship could travel there in half a year, it would have an average speed of 130,138,000,000 miles per year and a top speed of 260,276,000,000. If it carried enough fuel for the round trip to planet nine, and was planning to use a solar sale or magnetic drag to decelerate, it could accelerate to a speed of 1,041,104,000,000 miles per year.
Since Proxima Centauri is about 24,960,641,000,000 miles from Earth, it would take the Botany Bay about 23.975165 years to reach it. Since Alpha Ceti is about 1,463,622,000,000,000 miles from Earth, it would take the Botany Bay about 1,405.8364 years to reach it at a speed of 1,041,104,000,000 miles per year.
Put another way, a light year is about 5,878,625,000,000 miles. Traveling at 1,041,104,000,000, miles per year, the Botany Bay could travel one light year in about 5.65653 years, or about 0.1770999 light years per year.
So in 105 to 286 years the Botany Bay could travel 18.595489 to 50.650571 light years or about 0.0723559 to 0.2101683 of the distance of about 241 to 257 light years to Alpha Ceti.
So if the Enterprise was going to travel hundreds of light years from where they found the Botany Bay to Alpha Ceti and byond, it is hard to believe they wouldn't pass another harsh but habitable planet along the way to drop Khan's people off long before they passed by Alpha Ceti.
This theory also supposed that the hypothetical planet nine will be discovered and thus retroactively save the bacon of the creators back in 1966.
This theory also supposes that Marla McGivers would think of trips to distant planet nine (and maybe also ten and eleven?) when saying that interplanetary trips took years instead of thinking about trips to relatively close planets like Mars or Venus. If she meant that trips to Mars or Venus or Jupiter took years then DY-100 class ships would be much slower than if she meant trips to planet nine.
Anyway, I wonder what better answers you may be able to come up with.