Hmmm ...
Being old and slower of wit than I once was, I find it takes me a bit longer to figure things out than it used to. I think I begin to understand the X bit.
Under CT original rules as written, the E port was a "frontier installation" and the X-port was "no starport", and an X-port occurred on a random roll of 12 in the starport generation table. Pretty much same as what MCutter reports is documented for that page 432 of T5. (It should be noted that CT original rules didn't seem to be bothered with the idea of an A port at an uninhabited world). CT travel zones are up to the game master, and there's no required link between travel zones and starport type - not even X-ports.
Under CT rules as implemented in Supplement 3 (The Spinward Marches), ALMOST ALL red zones were given x-ports. The three exceptions are Andory and Candory (two worlds with space-faring Droyne populations under Imperial protection) and Djinni (an utterly uninhabited but habitable world with an E port, and I have no idea why it's red-zoned but habitable worlds with red zones and no people scare the willies out of me). There's one example of a X-port without a red-zone - Zeta 2 - and it shows up on me ol' paper sector map with, wait for it, a RED ZONE; in other words, it's an error.
Supplement 3 presents us with 11 examples of utterly uninhabited systems served by a "frontier port," and two uninhabited systems that have the distinction of being served by poor quality ports that offer unrefined fuel - in other words, D ports.
Meanwhile, Supplement 10 (The Solomani Rim), moved partly away from that convention. Again, every red-zoned world is X-ported - "thou shalt not land here" - but there are no less than seven examples of X-ports with no red zone, in every case an uninhabited world. All the uninhabited worlds in the Solomanii Rim are X-ports.
So, we have a situation where the game rules did not require a red-zone world to be an X-port, but it nonetheless became the original game milieu's convention. At the same time, we had two different treatment of uninhabited worlds: in one supplement they all had frontier (and better) port installations, in the other, they all had no port facilities. In that respect, the Traveller Map de-X'ing isn't doing anything Supplement 3 wasn't already doing except for its new treatment of red-zoned worlds.
Now, I like the red-zone with the starport theme. Helps with cases like Shionthy and Victoria. As to the Scouts deciding to make E ports on uninhabited worlds, here's my thought: if they're gonna call it a port, there needs to be SOMETHING there to justify it. Me, I'd say the standard is a landing beacon leading to some spot that's reasonably safe to land - the ground ain't gonna give way and leave you with your ship halfway in an underground cave, you aren't going to see trees grow up around the beacon, that sort of thing. And, there's a solar array with batteries, or a geothermal power source, something providing just enough juice that a single ship can plug into to keep the typical ship's life support going indefinitely, in case some unlucky travellers find themselves forced to land on an uninhabited world and wait for their ship to be logged overdue and a rescue effort to be launched for them.
If it doesn't have at least that, then I'd have to wonder what the scout was saying other than to plant a flag and say, "Kilroy was here."