I'm not sure I get what the problem is. This generator produces maps without any assumptions about the size of individual hexes. If there are too many hexes per map, you can choose a smaller map size. If after converting hexes into miles you get too large distances, you can select a different conversion rate (e.g. 1 hex = 4 miles instead of 6). If a specific value of the hex size is important for you (for example, if you need it for calculating travel time or something like that) you can force the generator to spawn more settlements, effectively reducing the average distance between them. Or am I missing something?