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I think they mean not under their own internally generated acceleration. If your ship thrusters are off you are "stationary."
Actually, if you are referring to the teleportation rules, since teleportation does not alter the teleporter's vector (which is why a falling person who teleports still goes splat, and why the sidebar says you cannot teleport onto a moving ship), I believe by stationary they mean that the two ships must be stationary relative to each other (must have the same vector). It is very difficult to match vectors with a ship that is able to change its vectors, so effectively, you need to cripple the enemy's thrusters to match vectors to board.
Starfinder doesn't go heavily into the drive technologies, but in many sci-fi settings (and in real life), the main drive is separate from maneuvering thrusters. In space combat, assuming the enemy isn't just going to blow you up and needs to or wants to board, a defending spaceship can use its maneuvering thrusters (or attitude control systems), which are often still functional even if the main drive is out, to impart a tumble. This makes it hard for spacesuited personnel or other ships to get onto the hull or dock. In Starfinder, it would make it difficult to teleport too, except that if you don't constantly change your tumble, I'd guess a teleporter could aim for the center point of your spin.
I can also see a Feat (or specialized training - Space Marines or special ops) allowing for teleporters to board a ship under power. While a boarding ship cannot match vectors with an unwilling target ship still able to maneuver for any appreciable length of time, a good pilot may be able to create moments of matched vector that a teleporter can exploit. It'd still be rough, and there's be a real chance of injury if the pilot or teleporter misjudges, or if the ship being board suddenly changes vector unexpectedly, but I could see it as something specialized troops might train for and employ
Another way to board a ship under drive is by stealth. In most cases, a ship will be either drifting on a specific vector, or if under drive, will be moving on a predictable course. If you could find a way to sneak up on the ship and match vectors without it knowing you are there, you could teleport on board.