I'm not exactly sure what the Modern Defense is. I think it's what we used to call the Robatsch Defense named after Karl Robatsch (October 14, 1929–September 19, 2000), a leading Austrian player and a noted botanist. What about the Pirc, named after Vasja Pirc (December 19, 1907–June 2, 1980) a leading Yugoslav (Slovenian) player?
ECO classifies the Modern Defense as B06 and codes B07 to B09 are assigned to the Pirc. My Modern Chess Openings, 10th edition, groups them together and calls it the Pirc–Robatsch Defense. As I understand it, the main difference between the Modern and the Pirc is that in the Modern, Black delays developing his knight to f6 which gives white the opportunity of playing c2-c3 which is supposed to limit the effectiveness of black's B on g7.
Transposition possibilities abound with either defense. After 1.e4 g6 2.d4 Bg7, in addition to being a Modern or Pirc, it can morph into a King's Indian, Dragon Sicilian or something else which means black simply can't apply the same strategy in all situations. Also, after 1.e4 g6 white can, besides 2.d4, play 2.Nf3, 2.Nc3, 2.c4 or just about anything reasonable move.
Another example is the King's Indian Attack. One site says the advantage of playing this is that it can be set up unhindered and it can lead to excellent attacking chances on the K-side. So can a whole bunch of other openings. I've been down this playing systems road. Way, way back it was the Stonewall Attack, then years later it was the KIA. I bought a book on it and the first thing the author said was white's strategy will be dictated by black's setup and there were chapters on how to correctly play against black formations like the K-Indian, Q-Indian, French, Sicilian, etc. Then there was the Torre Attack, another good 'system.' Guess how the book was arranged? There were chapters on how white needs to play against a wide variety of black formations. The KIA and Torre are decent openings, but they still required a lot of study and memorization in order to play them correctly. The same could be said of the Colle.
Back to the Modern...what if white plays 1. e4 g6 2. d4 Bg7 and now, instead of 2.Nc3 or 2.Nf3, he plays 3. c4. Isn't the game headed for a K-Indian with all its different options for both sides? Even though 1...g6 is universal, it seems like there is a lot of theory to be studied because black can't just willy-nilly play the same moves against anything white plays.
Even if white cooperates and plays, say, 1. e4 g6 2. d4 Bg7 3. Nc3 d6 4. Nf3 Nf6 5. Be2 O-O 6. O-O, arriving at this position:
According to my Rybka2 opening book black has 12 responses, the most popular being 6...c6 followed by 6...Bg4 and 6...c5. All three lead to a different type of position that will require different handling by both sides. Let's say black chooses the most popular 6...c6. The Rybka2 book lists 7 reasonable replies by white and, again, black's strategy will depend on which move white chooses. All this shoots down the idea that by playing the Modern, or any opening 'system,' you can avoid learning variations and a lot of theory. At least if you want to play correctly.
The following game by by a couple of class players demonstrates the point. Instead of transposing into the Old Indian Defense, black continues with a mishmash of moves seen in different defensive setups and soon gets into trouble.