I setup the min distance to 900 at first and changed it to 500 later, is this change too late or this is dynamic? Didn't find any yet :/

It is somewhat dynamic, but the min distance from any factory or buffer point is established when spawned, so by changing it lower you're mostly allowing factories to spawn closer to future spawned factories. For 30% of the time and at the 0,0 point, instead of spawning a factory, the game spawns a buffer point which no factory can be within the X distance of (being what X was when it spawned). The buffer points are there to keep the starting area clear and because in my original testing the factories would end up very grid like and this was one of the ways I could fix it and gave it a more scattered feel.

Each point is also generated with a minimum distance randomly between 1mindistance and 2mindistance, but the first buffer point is set to a full 2*mindistance and once a point is generated that mindistance doesn't change.

I've considered making it more dynamic, though that would require changing my data structure, but might be worth it. Anyway, because you set you minimum to 900, you wouldn't expect anything in a HUGE area around your spawn, at least a 1800 circle. If you want to get a sense for how large that is you can try this game command in a fresh game:

/c game.forces.player.chart(game.player.surface, {lefttop = {x = -1800, y = -1800}, rightbottom = {x = 1800, y = 1800}})

Can i spawn some with a creative mod to "correct" my mistake and then disabling the said creative mod?

I don't have a good way to correct it right now. I should probably make the setting more dynamic in the future. For now, my best suggestion is the current area you explored with the 900 setting is toxic. Even with the 500 setting the distances are going to be at minimum 500-1000 appart. But if that is the setting you want, I'd recommend just going in a straight line in a particular direction. That's also good advice to finding rich ores and it'll get you away from the no-mans land you created.

You could also potentially try removing the mod and loading/saving the game without the mod and then re-enable the mod. That might work to get rid of the established list of points, though I'm not 100% sure that'll work to remove all your current buffer points, but it might. Still wouldn't spawn any in your currently explored land though.