STA, Flight Centre, Harvey World Travel, One World or any other company who books travel would all be using the exact same product for the itinerary you have described. It just depends how many hours the travel agent is willing to use up on a booking that will get them very little in return for the large amount of effort and time. One World alliance is the name of the chain which the group of airlines like Qantas, Cathay Pacific, British Airways, LAN Airlines are linked to. That is the only way you will be able to get those flights on to one ticket that doesn't cost tens of thousands of dollars.
As for the offer of free date changes, you want to try and plan you trip as well as possible in terms of departure dates as availability in the special rtw economy class letter code is low at the best of times. This is especially important in South America unless you don't mind hanging around for another month or so as flights are not as frequent and often only one or two seats . I did read of a person who broke his leg in South America so wanted to change the date on his departure flight out of South America and due to rtw tickets on One World needing to be booking in L Class for Economy, he was unable to get a firm date for over a month. He was changing a fair way out from when he was originally booked so for over a month he has to hang around not being able to walk properly.
When I've done my RTW travels I have planned a fair bit of it but in overland sections allowed at least a week more than I believe I truly would need incase I discover something along the way or anything like that.
As for the South America leg of your journey, you have so many options but going South to Patagonia might be a bit of a bad time given it will be absolute freezing as. A good idea for you might be to get some brochures like a Geckos brochure on South America which has a fair few overland trips which will give you some ideas. If you are from the UK (or hold a UK passport) it will be a lot easier for you going overland because places such as Paraguay and Brazil which require pre-arranged visas for most major countries like Australia and the US give free visas on arrival. If you wanted to do some very major backtracking after landing in Santiago you can do a bit of travel through Chile and Argentina before returning to Santiago, fly to Easter Island and then try and get a flight back to Santiago and on to Lima with a 24 hour period so as to constitute a transit rather than a stop over. After landing in Lima make your way overland through Peru, Bolivia, Paraguay. This might mean a bit more on your ticket in terms of cost because it may mean you have to pay for one extra stop in South America, but it would be worth it to see one of the places that is a once in a life-time sort of place. To do that you'd want the continent based fare on the One World alliance and that's the one you should be looking at anyway as the mileage based one will restrict you a lot more. You can get some mammoth mileage for frequent flyers if you are creative with your itinerary on the continent based fare and use airlines other than British Airways and American Airlines whereever possible.