The values you see are true whether you have bonus' on the terrain or not. IE, they won't do you any good just like you've been reading.
I'm not sure if I am misreading you but something is not quite right here.
If I just concentrate on shields for the moment to simplify things. If I settle on an iron hill, I get
2 shields from the city tile as opposed to 1 if I settle on a standard hill. I cannot develop that tile any further but I do not lose the +1 iron bonus so what's the problem? In fact I might actually
gain from settling on that tile short/mid-term as it may be a food poor site and I might not actually be able to work that iron hill for a very long time. I also gain access to the iron straight away. That's normally good as long as you are not worried about repeatedly connecting and disconnecting your resources. (This 2 shield core also applies to settling on other tiles that have a base shield value of 2 such as plains cattle and furs on plains.) I therefore assume that the 'base' that is in your earlier quote includes the modifiers for bonus shields.
However you do lose out on settling on bonus grass tiles (or other 1 shield base tiles, such as furs on grassland) until they grow to city size. A town on a bg gets the same shields (1) as a town on a standard grass tile. However a
city on a one shield base tile gets that second shield so it is only a temporary loss if you intend for that town to grow. This is the only situation where you have a short term loss, in that an extra shield is created for towns placed on tiles that have no base shield value, such as standard grass. This is not a factor though when comparing sites that are cities or metros.
I've never looked too closely at the finer points of commerce but I do know that your towns will get a commerce bonus of some sort if you settle on a high commerce tile, such as golden hills or high value luxes. However I have got a game that I am currently playing where I chose to settle on a spices tile. Again there is no net loss of income as the city centre has the +2 commerce bonus associated with a spice tile. The difference is that by settling on the lux had access to the bonus commerce and lux straight away. I also have a city on a golden hill which has kept the +4 commerce bonus for the gold so I cannot see how I have lost out on commerce either.
I do not (or at least very, very rarely) settle on food bonus tile though because the extra food is lost. The city centre tile has a basic value of two food for a non-agri civ no matter where you settle.
I too am a liitle confused as to why a strat guide might advise you not to settle on resource tiles, DarthJedi! Personally I'll place my town where I want it, no matter whether it has a lux/strategic resource on it or not. Indeed I'll often place it on the resource to gain access to it straight away; especially if it is on a jungle tile. I may miss out on the odd shield before the towns grow to city size but as not all tiles in the area will be worked anyway the loss will not necessarily be that great. You only lose if you are working a grass tiles before it grows to city size. If the site has a few bgs around the loss will not be noticed and when they grow to city size there is no difference.
End result. Don't settle on food-you'll lose it. Don't worry about loss of commerce. Shield bonus: you may lose out in the short term compared with settling on a zero shield tile instead but any losses will be returned once it gets to city size and maybe you wouldn't be working that tile before then anyway.
I could of course be missing something so I am happy to post specific examples if someone can see a hole in my argument.
Edit: sorry MAS, I didn't see your post. Much more concise!
