The apertures that I highlighted above with an arrow are never seen emitting an exhaust plume at all but seem likely to be another part of the vertical thrust or manoeuvring system — possibly the primary system.
To be clear, I do not think that one of the greatest children's television series of all time needs apologists, but this Facebook argument might be of passing interest to fans of the show.
"One of Gerry Anderson's biggest mistakes was that Thunderbird 2 when docking [sic] did not need vertical thrust until it ceased forward motion."
I think this nitpick must be laid at the door of the special effects team (members of which went on to work on little-known projects such as 2001: A Space Odyssey, The Empire Strikes Back, Alien, The Spy Who Loved Me, Moonraker, For Your Eyes Only, Superman, Batman and GoldenEye), rather than Gerry Anderson personally.
Regarding vertical thrust, it is often shown (including in the 1960s movies, which are the most recent canonical source with highest production values) that both Thunderbird aircraft can hover without using their rocket engines. They make an audible jet whine when doing so. It makes as much sense to complain about the lack of rockets as it would to complain that Thunderbird 2 doesn't fly in a nose-up attitude to maintain slow-flight airspeed when escorting Alan's Tiger Moth biplane. It seems safe to assume that the Thunderbirds don't have the same constraints as conventional propellor aircraft.
Also, given that International Rescue are extremely secretive and it is established in the second movie (Thunderbird 6, 1968) that Brains invented actual anti-gravity technology, I wouldn't worry too much about the floating.
"But if Thunderbird 2 can hover by anti-gravity why have downward jets fire just when forward motion ceased?"
This could be a feint to conceal the actual technology in use, it could be done to generate a smoke screen, it could be a routine or automated action, e.g. to check the launch system is operative before landing, or (by far the simplest explanation) simply a transition of the vertical thrusters to a higher-thrust mode of operation.
If you think about it, it would be very dangerous and/or embarrassing if the launch rockets were to malfunction. Testing them could easily be a mandatory part of the pre-landing checks, along with checking that harnesses and hatches are secure, and that the fuel level is sufficient.
The apertures that I highlighted above with an arrow are
never seen emitting an exhaust plume at all but seem likely
to be another part of the vertical thrust or manoeuvring
system — possibly the primary system.
Maybe some aspect of the technology normally used to maintain altitude at low air speeds is unsuitable for use in ground effect. For example, VTOL aircraft can suffer from hot gas ingestion (HGI), which causes loss of thrust when jet exhaust is deflected sideways and/or upwards upon striking the ground. Look at the proximity of the highlighted exhaust nozzles (if that's what they are) to the main engine intakes in the above photograph!
Another real-world phenomenon that VTOL aircraft designers must contend with is suckdown. Jet exhaust sweeps along (or entrains) some neighbouring air; more so when close to the ground. In the case of vertical jets, this can cause downward airflow over the fuselage which reduces the air pressure beneath. Again, look at the absence of strakes to mitigate suckdown in the above photograph.
There is a similar pair of unexplained apertures at the rear of the fuselage, visible in this photo of Thunderbird 2 without its pod:
It seems reasonable to assume that these apertures serve the same purpose as those near the front. If they are indeed thrusters, then they would be too close to the ground to be used for take-off and landing. (Probably also a consideration for the special effects technicians.) This would explain the necessity for auxiliary rockets beneath the twin booms.
Here's another common nitpick:
If TB2 needed a ramp to take off from the island, how did it manage everywhere else in the world?
Obviously, the answer is that Thunderbird 2 takes off more slowly everywhere else, using precious vertical thruster fuel instead of its main engines.
Aircraft can fly up to 25% faster at high altitudes where the air is thinner. It is critical for Thunderbird 2 to reach a high altitude as quickly as possible in an emergency. (This is also the reason that Thunderbird 1 launches vertically like a ballistic missile before changing to horizontal flight.)
In my opinion, this question is rather like asking "If firefighters need to slide down a fireman's pole in a fire station, how do they manage to walk downstairs normally everywhere else?"