Kuroyuri does not appear to have been part of the Kingdom of Mistral, but was independent. Mistral police flights do not fly over it as part of their patrol route, and it was only the 'smoke' plume from the dead Nuckelavee that attracted by chance the attention of a pair of airships. As well, the Nuckelavee was still alive 10-12 years after the desctruction of Kuroyuri. I can understand the village being destroyed, but if Kuroyuri was part of Mistral I have trouble understanding why the Nuckelavee was not hunted down and destroyed shortly after by Mistral. If Kuroyuri was independent, then it's a case of 'not our problem' on the part of Mistral.
However, Kuroyuri is not that far from the city of Mistral, as seen by the shortness of the flight. The airships weren't moving that fast, as Ren and Nora were sitting out in the open with little discomfort. Perhaps Kuroyuri and Mistral are close 'as the Qrow flies' (sorry), but the road connecting the two takes a significant detour. There is a small range of mountains between the two, as well as another settlement along the route, Kuchinashi. It's possible that the road winds for a quite a distance because of the mountains before reaching Mistral. I suspect that this mountain range is the southwest boundary of the Kingdom of Mistral, and that Kuroyuri was the first settlement across the border.
Oniyuri must have been fairly close to Kuroyuri. Venom is of little use if it doesn't work quickly, so I have trouble believing that any major length of time passed between Qrow being attacked and arriving in Kuroyuri. As Qrow was in bad shape when team RNJR awoke the day after Tyrion's attack, I'd say it's likely that they reached Kuroyuri that same day. As Qrow was on a stretcher, I'd be surprised if they travelled more than 20km that day. As Ren said that his parents were part of the scheme to create Oniyuri, I suspect that the two communities were founded at the same time.
Higanbana must have been a considerable distance from Oniyuri, as team RNJR did not take Qrow back that way. This suggests that they knew he would not survive that many days, and that his only hope lay in moving on. It also means that there is nothing between Oniyuri and Higanbana. Higanbana is the only large settlement mentioned, and yet it lies between Shion and the Nuckelavee's lair. Could the Nuckelavee be old enough that it has learned which settlements are too large for it to attack, and so it has left Higanbana alone?
Shion is an unknown distance from Higanbana, so there may be additional villages between the two that RNJR passed through. As there was no word from Shion at the unnamed village since the CCT went down, it must be a good distance between the two with no other settlements between the two to pass on news.
When Yang arrived in Mistral, she was able to cover a lot more ground by riding Bumblebee. Since she could move faster, she didn't have to follow the same route as team RNJR, who would have taken a route that may not have been the shortest route. RNJR may have been taking a route that would go from village to village to obtain supplies and find shelter from time to time. Yang could instead take a shorter route if it existed. We have no idea where the Just Rite staion was, but it's unlikely to be near Higanbana for example, as the bartender says there's not really anything 'out here'
The curious thing about this part of Anima is that it has train service! On the display boards for the Mistral Central Station in V6C1, trains to Shion are shown on the departures board, leaving at roughly hourly intervals. Even though there was no mention of trains in Shion when team RNJR was there looking for transportation. It makes you wonder why Mistral would build a line that far outside their boundaries, and what happened to cut off the service so that RNJR had to keep walking.