There are many differences between the original "Metal Gear 2: SOLID SNAKE" on MSX and the version included in "Metal Gear Solid 2: Subsistance". In the 2006 version of "Metal Gear 2: SOLID SNAKE" they changed the portraits in the "codec calls" with Yoji Shikawa's artwork, and they also added a new line in Gray Fox's speech after you defeat him:

In Japanese
その時、俺は耳も鼻もそがれ。。。ひどい状態だった

In English:
"They had cut off my ears and my nose, I looked terrible"

These new words fit perfectly with Ishmael's bandaged face in Metal Gear Solid 5.