The logic for the Navmap is somewhat counter-intuitive and has some questionable design decisions. There are a few factors that determine the size of a system map or where they will be positioned in the universe view.
Inside the universe ini file, you have two main types of section header. These are [Base] and [System]. As you'd expect, the system header is the one that carries data relevant to the system, and by extension, the Navmap. The position of a system's icon on the Navmap is decided by the “pos” value.
The pos key takes two values. These are technically floating point values as they can be decimals, but this causes strange behaviour in base game Freelancer, where your ship icon may appear in a different location to the system you are actually in. The two values correlate to an X and Y coordinate on a grid.
It's possible to place multiple systems on the same X-Y tile, but only one will be clickable.
Each individual system has it's own Navmap scale. This allows for the Navmap to be more/less zoomed in for when the objects are spaced out / close together. It is defined by the “NavMapScale” ini key, but the word scale is rather misleading.
The way FL calculates a system's scale is it takes a base value and then divides by the scale provided, rather than multiplying it, as one would expect. If left blank, the value defaults to 1.
Unless modified, Freelancer has the default scale for the entire system (which is split into an 8×8 grid) set to 150,000m (150k). This would then give an individual grid size of 30,000 (30k). This is with a scale of 1.
Here is the difference between a scale of one or two:
|Scale||Individual Grid Size||A1||B2||C3||D4||Origin||E5||F6||G7||H8|
If you had something with the exact same X/Y coordinate, it would place itself within the grid of whatever is listed above.