My take on how mission 1 is supposed to work:
Both the cubes and the bullseyes have red surfaces which net you a lot "extra" points when shot. There's probably a trick to the octahedrons and the squares too, but i didn't figure it out. If you make sure to take a hit every couple Zombies, you should be able to one-shot-headshot them consistently. (This adaptive difficulty is total nonsense)
You get +5 seconds for a Zombie and +7 for a dog. Getting spotted by a Fattie means your run is over, even if you dodge every charge they are too disruptive. Dogs are a must-kill if you run into them, they stick to you way too good.
There is a whole bunch of cubes in the last room before the exit beacon.
I'm almost certain it is theoretically possible to plot a route past enough points to unlock a grenade fairly quickly. Using that, you would explode the followers you collected and gain much extra time at once. Then, continuing to follow a route you plotted and optimized before, and hitting everything for the bonus points, one should be able to unlock the weapons.
On the other hand, i have the sneaking suspicion this adaptive difficulty was the last thing he added and he definitely didn't playtest a full run with it, if he did that at all. Mission 4 (old Mission 3) is a crapfest.