[edit] So my original answer was confusing as heck, and there are some incongruencies in the many answers you find on this subject all over the internet; so, let me try this again:
Part 1: Why they are Different
if([]) and if([] == true) are not the same operation. If you see the below example, you will get the same result when doing the same operation.
//Output: false
if([] == true) {
console.log(true);
} else{
console.log(false);
}
//Output: false
console.log([] == true);
Part 2: Why it matters AKA: the confusing bits
In JS, the following is a common expression used to see if an object/variable exists:
var foo = "Hello World";
if (foo) ...
From a design perspective, this test is not important to see if foo is equal to true or false, it is a test to see if the program can find the object or variable foo. If it finds foo, then it executes the results in the "then" condition, otherwise you get the "else" condition. So, in this case, it will convert foo to either false for does not exist, or true for does exist. So in this case the string is reduced to a boolean.
In contrast:
var foo = "Hello World";
if (foo == true) ...
Is typically trying to find out if the value of foo actually equals true. In this case, you are comparing the value of foo "Hello World" to a boolean, so in this case, "Hello World" does not equal true.
Just like foo, [] can be evaluated more than one way. An empty array is still an object; so, in the first case, it coerces to true because it wants to know if [] can be found; however, [] also equals ['']. So now picture this:
if (['bar'] == 'bar') ...
In this case, JS will not look at ['bar'] to see if it is there, but as an object containing a single value which it can convert to the string, 'bar'.
So:
if([]); // is true because it is an object test that evaluates as (1 === 1)
and
if([] == true) // is false because it is a string test that evaluates as ('' == 1) to (0 === 1)