What is the material difference between iPhones ordered from different countries?
There is no difference in quality whatsoever. 

The only difference is that the actual phone hardware (the small bit that creates a phone connection) will be different to work best in the country where you purchased a phone. A US phone will work with all phone networks in the USA, a German phone will work with all phone networks in Germany, and a Malaysian phone will work with all phone networks in Malaysia. They all will work fine in many other countries as well, but possibly not in all. 

Plus, because the laws in various countries are different, that may cause differences. Obviously that Malaysian phone has to conform to Malaysian laws, but I wouldn't know if that makes any difference.