Oh no, I was almost sure I fixed the orange gel and energy turret popping up too early.

They are not supposed to be active till the last stage, where the
blade is lured up into the pipe to break it. I shot energy balls, rockets, bombs, anything I could think of and it wouldn't break in the 2nd stage while final testing.

the energy turret is only meant to be active in the last and quickest stage, where you shoot across up to the final explosion button. During this stage, you are standing behind the central pillar, where most energy balls can't get you, or you can crouch and let them fly over your head. Also, the metal covering over the orange gel should have broken as it fell if it had fallen after being hit by the blade a few times, but probably did not due to the way the bomb seems to have hit it and broke it instead.
Also, this boss is supposed to be much different than the portal and portal 2 bosses, and it is harder as well. The pattern in stage 1 is as goes: the arm will attempt to fling you around the room, attempting to get you to press the buttons to override its security measures. Meanwhile, every 9-16 seconds, the arm will freeze in its place and the energy balls it has stored will launch around the room, hitting you or bouncing off off a nearby surface. The arm has some specific locations around the room it will attempt to launch you, which are randomly chosen.
Stage 1 is supposed to consist of only the arm, HEP, and buttons.
Stage 2 is supposed to consist of only the arm, bombs, and white gel.
Stage 3 is supposed to consist of only the saw and white gel.
Stage 4 is supposed to consist of the saw, white and orange gel, button, generator explosion, and energy turret.