Number of cities affects rate increase of mind mana.
It would appear that mind mana gives ~3% * (number of your cities connected by roads).
I was looking through the c files and noticed it loops through every single city when doing the commerce rate modifiers. So I went into a game and spawned a bunch of settlers, and each city I created that was on a road connected to my other cities added about another 3% to the research rate modifier given by mind mana.
I'll admit I dont know exactly where it's happening, but here's how I've gone through the code so far:
CvCity:

rocessBonus(BonusTypes eBonus, int iChange)
CvPlayer::changeCommerceRateModifier(CommerceTypes eIndex, int iChange)
CvPlayer::updateCommerce(CommerceTypes eCommerce) <-- noticed this loop:
for (pLoopCity = firstCity(&iLoop); pLoopCity != NULL; pLoopCity = nextCity(&iLoop))
{
pLoopCity->updateCommerce(eCommerce);
}
I'm going to guess that it when it loops it hits that update function and each time it has a city with access to mana, it adds an extra 3% (and then every city ends up with 3%*# of cities). But I'll see if I can't figure it out exactly.
EDIT: Or if I had realized what I was looking at in the process bonus part I would say it's just cause that gets run for every single city, and the modifier are running on CvPlayer which I'm assuming makes them global so each city gets the previous city's bonus. FYI, it looks like heal rate and the earth mana bonus are done in the same way, so I'm going to assume the same process is affecting them as well.