A few things:
The bonus is currently slightly bugged. The maximum distance was improperly entered and should be fixed when the next round of strategus modifications comes in. But you are correct in that 100km is approximately what it should be for 70%. When the system is fixed, you should see a slight increase in trade bonus across the board, though the difference will be most significant in the second half of the chart.
The goal of the system was to make a differentiation between fiefs. Some fiefs are more valuable for selling goods than others, you are correct, and that is entirely intended. Those fiefs aren't as good. They aren't as valuable. The people who own them are disadvantaged, at least in the realm of trade. This disadvantage is perhaps countered by their central position and ability to control trade routes, and perhaps not. However, if they are truly disadvantaged, good. Let the owners of those fiefs fight for a more favorable position.
As to the affording of horses, the next strategus patch is also intended to feature an overhaul and general price decrease for the crafting system, which will result in the ability to produce horses much cheaper. Currently, though, someone with a 40% price discount on Rounceys would be able to produce 100 for 21624, a sum which is easily obtainable after a single caravan journey of 100 troops. (50 crates times 6 goods per crate times 80 goods price = 24,000 gold, and that isn't even a maximum efficiency trip).
As to the problem Keshian brings up about large alliances, that is a wider problem than trade bonuses and will hopefully be dealt with shortly. However I do not believe the trade system should be modified accordingly. The system is designed to give rewards to those who take greater risks, and I would much rather fix it by increasing risk for everyone than decreasing it for everyone.
But for the TLDR crowd, I guess what I am trying to say is: Tomas, what you bring up isn't a flaw but a feature.