This still seems to be the wrong way round. On larger maps you get a greater penalty for distance.

Do you have any more details on this? I wasn't aware of this problem - I always play large/huge maps, so this definitely affects me. Is it something that can be modded in XML?

Well I haven't got BTS yet, but this is what I found in Warlords and the ref guide shows the same situation for BTS. Look at the dist maint multiplier for map size on page 75 of the guide. It increases from 0.5 in duel to 1.0 on huge. The same way it increases as you increase difficulty from settler up to Deity level. I changed the XML myself when I played warlords and it worked as I've explained. As it stands on a small map you can afford to spread out more. On a huge map you need to keep your empire tighter.