the fact that the unbought singular rewards didn't change colors When I used up my achievement-points on the timers it led to me incorrectly conclude that they were inactive. (most games I've played with a similar reward/upgrade system gray the rewards/upgrades out when purchasing power is zero/below minimum)
Invisible? How do you give people incentive to reach their requirements then? You need them to know of their existence for that. (at least show an X-rewards-locked count)
The only rewards that aren't visible are ones that affect races that you haven't unlocked yet. e.g. If you haven't unlocked the undead, then you won't see 'Unholy Alliance'.
Maybe I didn't understand your problem. Did you have achievement points available, but clicking on a reward in red (in the screen after starting a new game, not the one you get to through the achievements screen) didn't do anything? Someone else had that issue a while ago, but I was never able to reproduce it or find a potential cause.
You have to start a new game to get achievement rewards, which resets all your buildings and resources. Each reward costs 1 achievement point. Rewards that have multiple numbers cost 1 point per number, and you have to get them in order. Reducing the fight cooldown costs 1 point per second. I have to rearrange the achievements screen for the next achievement update (which will hopefully be out in a couple days) so I'll put some more info about getting rewards in there.
 "Lazy Kings"){kind=icon}
 "The Life of a Developer"){kind=icon}
 "Crafting Idle Clicker"){kind=icon}
 "Milk`It"){kind=icon}
 "Gold City"){kind=icon}
 "Idle Necromancer"){kind=icon}
 "Death Squad 2: Idle Space Raiders"){kind=icon}
 "Billionaire President"){kind=icon}
 "Sword of Storms"){kind=icon}
 "Belial Chap.3 Ars Arcana"){kind=icon}
 "Persist"){kind=icon}
 "Graham Clicker"){kind=icon}
 "Elevator - Clue"){kind=icon}
 "La Grotte du Geek"){kind=icon}
 "Pieces Nightmare 4 (relaunch)"){kind=icon}
The only rewards that aren't visible are ones that affect races that you haven't unlocked yet. e.g. If you haven't unlocked the undead, then you won't see 'Unholy Alliance'.