It's all basically the same thing
 

-After so long a discourse on the X theory and the Y theory, we know that it's all the same thing/they are all the same thing.

Are they both correct? If not, what are the rules we have to follow in using 'it' when talking about more than one thing?(Meanwhile I will try to hunt down more examples of this kind)

p.119
-But none of this is why Bryan Garner is a genius.

The correct way to say this is: After so long a discourse on the x and y theory, we now know they are both the same.
They instead of it's all is preferred because you are comparing only two things.

Thank you. But do you mean when there are more than two things, we have to use it's all:

p.175
-[...]to try to shut your head off so you can hit the rack at 0130 and get up at 0600 and do it all again.

1. He is talking about a whole bunch of things; why it not them?

2. What does hit the rack mean? I know hit the road, hit the pool, etc. but not that.

Do it all again refers to a routine. The series of things done becomes singular when it is thought of as a routine.
I think hit the rack means to go to bed.

Thank you.

There are many slang ways to say "go to bed/go to sleep".

The word "rack" has many slang meanings, including "bed"; this meaning is common in US military slang, especially the Navy and Marine Corps when referring to beds on board naval ships. Similarly, "rack time" refers to "sleeping" and/or to the period when individual crew members are off-duty and able to sleep, and "to rack out" is "to sleep" or "to go to sleep".

Excellent answer. Thank you.