The problem with your math is that there is no indication that the total free company size is different per server. X people in a FC x 25K is the same on a high pop server as it is on a low pop one; exact same buying power.
The problem for SE is that there are more FCs with high member counts on high pop servers, which would allow more houses of a given size to be bought -- SE can't support a house for every free company, so they have to raise prices.