Birkat hamazon is said after eating bread. In the first paragraph, the word "lechem" - bread - is mentioned. The first paragraph, overall, thanks G-d for giving us food.
"Me'en Shalosh" a shortened version of Birkat Hamazon, is said after eating cakes, cookies, etc.; after eating one of the 7 fruits of Israel or after drinking wine. It too makes mention of the food eaten / drunk ("michya", "gefen", "perot")
"Borei Nefashot" doesn't seem to mention anything about the food eaten or even the act of eating or even a general topic about G-d giving us food. It says, "You have created living things ... to keep other living beings alive..." (loose translation of the concept>) It seems to be an indirect reference of the concept that one animal eats another animal. Also, we say "Borei Nefashot" on most fruits and vegetables as well as many other foods that are not "living beings".
So, what, exactly, in terms of what we ate, are we thanking G-d for in Borei Nefashot?