In 1.2 there is a logical explanation for the so-called "exploit" as long as you accept that a thruster speed limit exists. However, in 1.3 a magical rocket fairy comes and slows down your ship to make sure you aren't going too fast for a pirate/griefer to catch up.
The same explanation can apply as before, only with slightly altered effects.
I'm assuming hyper jump and supercruise are variants of the Alcubierre drive, with a bubble of warped space moving around at great speeds, not the craft relative to space. Whereas locally driven thrusters use the same fuel, but via a cleaner, more efficient version of old-fashioned chemical propulsion.
There might be many reasons to limit speeds in relative space, such as:
- micrometeorites and kessler syndrome debris might puncture shields/hulls above a certain speed and by keeping it under, avoids catastrophic micro impacts, or the very structural beams the hold the ship together will vibrate with enough frequency to tear themselves apart above a certain speed. (ie. pure engineering design reasons)
- lower level relativistic effects might cause time dilation (aka server lag) without the accompanying space-time bubbles and universal time is impossible without preventing all ships to confirm... think of speed limits like a calendar- an earth day has 24 hours. a KM traveled is relativistic, but the maximum possible speed limit might determine the length of a "space day" which would need to be relative (avoiding relativistic effects, give uniform time to all humans)
- Engine technology for FDL... is this explained anywhere? Anti matter is probably involved in order to create the energy needed, meaning there's most likely some kind of magnetic anti-matter containment in the FDL/Power Supply and if it goes above X speed, it could destabilize a containment field and cause a matter/anti-matter reaction (physical reasons from inside the ship, not from without)
- maybe going that fast creates G-forces that would create micro-fractures in the human anatomy that build up to kill a man over time because man evolved under a specific set of speed/gravity requirements- while the G-forces would be minimal in deep space, there is still the tug of dark matter anywhere within the galaxy, which is strong enough to make sure stars at the edge of the galaxy go just as fast as those at the center, so by travelling fast enough without altering space, it might be possible that these background forces gain enough energy to "plop" out the very molecules from within you as they collide with the invisible sub-space gravity fields... as your DNA slowly degrades by loosing atom after atom, you begin to suffer the same symptoms of radiation poisoning. perhaps early colonization attempts made before hyperspace via combination of cryo-sleep and long-distance under-lightspeed journeys resulted in brittle and feral humans that could not then stand on their destination planet and there are roving ships of ancient devolved humans full of incest and genetic deformities lurking about in the black, waiting for some unlucky pilot to stumble upon them and investigate, only to become their dinner. (the biological rationale)
All in all, I think they are talking about "boost speed", not "max speed without boost" which makes sense for gameplay, as otherwise there's no way to catch someone, but you could just as easily chose:
a) complain about "real physics" in a video game
b) come up with creative sci-fi solutions that add to universe