I could almost set my watch by how often we get this question.
Bottom line for a foreigner it does not matter. The number you get from the IRS (your rut number), will be used for all other purposes including your RUN number or ID number. It even says RUT on your identity card now when you finally get residency.
There is whole section on it in the the Chile Wiki
http://www.allchile.net/chilewikiand there are some articles about it on
http://www.allsouthernchile.com Both where written by my wife who is an attorney.
A word of warning to everyone.
The consulates are NOT authorities on anything and they are not attorneys. The people that work there are not qualified to give legal advice, are rarely correct when they do, and in the rare case they are qualified (you won't get to talk to one of them), they have no official authority to do anything. The authority will ultimately be with ministry in charge of whatever it you want to do for example the IRS for your RUT number, civil registry, or immigration for immigration issues. What ever they tell you is in no way official, and is subject to change in Chile.
They are not even the final authority when trying to do simple things like notarize and legalize a document outside the country. We still have to run them through the foreign ministry once they arrive in Chile to be authorized. We have seen so many people get themselves in to a mess taking advice from the desk clerks at their local Chilean consulate. I would say about 30 to 40% of all the documents we get from the consulates have errors and mistakes, and we deal with dozens of them around the World every day.
We have also seen people have their immigration applications rejected, because they listened to the advice of the consulates.
They are under staffed in many places around the World, in favor of the ambassadors wife getting antique French furniture in her house. For example, Switzerland only has two people working the front desk handling notarization. Yet, every single banking transaction and other legal document involving Chile must be run through that office. Switzerland? With all the copper trading going on, and likely half the countries GDP has to use that office but there are only two people because it is really expensive to maintain staff in Switzerland.