Glaukos |
A suit of heavy armor filled with water walks into the room. A tiny cuttlefish swimming inside the helmet wiggles a few tentacles, and imparts some technical knowledge telepathically.
Armor Prototype Proficiency has two parts, which are separate benefits. The first one makes you proficient with heavy armor. That part works exactly like any other armor proficiency.
The other benefit improves the hardness, HP, and saves of your prototype, regardless of which category of armor it is.
Note that in the paragraph just before Armor Prototype Proficiency, it states, "Your armor prototype works as normal for a suit of its type, but it also gains specific benefits based on your mechanic level, as defined below" (emphasis mine). So your armor prototype is either light or heavy (or powered, at 5th level and above), depending on what specific suit of armor you modified to make it.