You know, you might be able to replace negative matter with real life antimatter. Shouldn’t be too much different, but with a side effect of a planet sized (or bigger) explosion if it crashes. Perhaps this is why you wait until far away from planets to use FTL travel?

Gravity wells screw up the navigation and at FTL speeds that ain't a Good Thing.

In the rater famous Honorverse ships can only enter hyperspace at a certain distance from a gravitational source. It is not explained why it is so, and nobody cares. None of the characters is a physicist; it doesn't matter why, it only matters that this limitation exists.

Also, @AlexP makes a really good point. Authors sometimes get stuck on trying to explain every detail when every detail is not (and will not be) required for the story. If you need this explanation for your story, telling us why it's important to your story will help narrow the question from an off-topic infinite list of things to an on-topic finite list of things.

When in doubt don't forget those reliable real world reasons why we aren't supposed to do some things : (a) the government made it a regulation (who knows why ?) and (b) the lawyers said so (again, who knows why ?).

If you want your story to fit known theoretical physics, there's a problem with the Alcubierre solution, pointed out in the "Physics" section of Alcubierre drive wiki--if the exotic (negative) matter can't move locally faster than light, devices have to be placed along the entire path in advance to distort the spacetime in the needed way as the bubble passes each section of the path. See discussion on p. 3 of Everett and Roman's paper at arxiv.org/abs/gr-qc/9702049 and also starting on p. 119 of their book "Time Travel and Warp drives"

Couldn't the ship simply be too big to land? Like in every Star Trek series except Voyager.

Superheated plasma ring held by a magnetic field simply isn't going to work in an atmosphere (there's many reasons why the fusion reactors we're trying to build all work with a vacuum far more empty than actual space). Do you really need another reason why you can't use the FTL drive on a planet with an atmosphere?

JBH. Ok let me be even more clear about how the Drive works. It’s built around the concept of Heavy Matter - basically an exotic form of matter made of significantly (like about 18 orders of magnitude greater mass) heavier nucleon counterparts; so heavy that gravity actually becomes significant at the subatomic level, allowing for the construction of elements with absurdly high atomic numbers. Argosium is a very specific Heavy Matter element that, when its density decreases, begins to emit radiation which can convert ordinary matter into Negative Matter. (continued)

(continued) as it does so, its nuclei convert back into ordinary matter, causing them to almost instantly be destroyed by fission. So the Argosium is turned into a superheated plasma so a) it’s very rarefied b) it will emit high levels of this radiation. Negative Matter, in my conception, repels ordinary matter and attracts Negative Matter. This isn’t what would actually happen if General Relativity is 100% correct in that area - in fact, the Negative Matter would repel ordinary matter while being attracted to it at the same time, resulting in them chasing each other forever. (continued)

(continued) That’s not impossible because it doesn’t break any physical laws, but I don’t want it in my conception. So I cheat a bit, and say our current understanding of mass doesn’t really apply to negative mass (plausible considering it’s based entirely on the positive kind) and so it repels ordinary matter. Tungsten is used because it’s incredibly strong and can withstand high temperatures without melting, indicating its intermolecular bonds are strong - even as negative matter builds up inside, repelling all the ordinary matter around it, the ring will retain its structural integrity.

So to fire up the drive, you heat up the Argosium plasma, tungsten starts to be converted, once you go over a specific negative mass value, a warp bubble is created around the ship. Now, there’s another Heavy Matter element which is key here - Salirium. Salirium is an element that a) attracts Argosium very strongly b) neutralises warp bubbles when they pass through it. When the warp bubble activates, all outside forces disappear - except for the attractive force of the most attractive source of Argosium (which could be several light years away), starting to pull the ship in that direction.

Constructed around near-Earth space are a series of ‘beacons’. A beacon is basically an enormous cube subdivided into huge tanks of liquid Salirium. A warp ship will propagate to the nearest beacon, and drop out of warp as soon as it passes through the space occupied by one of the tanks. The resulting explosion - a violent burst of near-c particles produced by the ship as it lands - is absorbed by the enormous tank of liquid metal. (continued)

Heavy and negative matter violently react when in close proximity, converting each other back into ordinary matter. The result is that the negative mass in the tungsten ring turns back into tungsten as it’s immersed in the Salirium pool - the tank is then drained, allowing for the passengers to disembark. Now, the beacon system essentially acts like a train line. If the engine is fired up enough, its warping will be strong enough to pass through a Salirium tank without being neutralised - so a ship can pass through all the beacons on the straight line path between them, then stop at the last.

JBH again - there is a story reason why I want this to be the case. Basically, I’ve plotted out a scene where a planet is being ensieged from space, and its inhabitants are unable to flee because any ship that leaves the atmosphere is instantly destroyed. I need a reason for why they just can’t warp away on the surface, especially since this sequence is critical to the plot.

To those saying "Just hand wave it, forget the details, no one cares". This is A perfectly valid approach (and the most common one) in science fiction. But in this case is obviously not what the OP intends, they are trying to write one of those Science fictions where the technical discussions about "how this works" ARE one of the main points of the story. These stories do exist and that is nothing invalid about them.

Grant Garrison - Real life antimatter can produce a lot of energy, but it can not get you past the speed of light by any known physics. Negative matter (if this mythical hypothetical existed) could in principle get you faster than light.

What happens to high speed objects (from external observer) that approach the warp-bubble?

It's much easier to produce a stable plasma in vacuum.

FTL is implausible anyway so you can just wave your hand and have it behaving the way you want