Shown cost is the cost per firing one employee at the department, not times how many you fire at once manually, I agree this could be better, but it also shows the rewards for a single employee. Your auto firing rate may be different than the manual rate and I wanted to show baseline values for both.
There is a known dead-lock that can occur if you never buy a single auto-fire upgrade. One department near the very end the firing cost ends up very high because it's a department with 500 employees after firing several departments with 1 employee in a row. You never get enough fire points back from the last ones to get rid of 500+ in one fell swoop. With 1 auto buy it fires one or more employees for free and you get back enough to manually fire people again.
Popups are a core part of the game and will occur every playthrough no matter how many times you restart. It was designed on purpose to be semi-annoying and forced as part of the social commentary of the game. If you were the president and clearing out people with reckless abandon you should pause and reflect on your actions and the damage it is causing.
I appreciate the feedback and some of these points will be addressed in the next update