In the "Format" page of Math Help, it's written that:
The standard centralized formulas can be aligned to the left without using the Format - Alignment menu. To do this, place an empty character string, that is, the inverted commas which surround any text "", before the section of formula that you want to align.

But is the "empty character string" really empty??

Let's try this reduced case:

X = ...  newline
""X = ... newline
alignl X = ... newline

It is obvious that the second line is shifted a little bit to the right, meaning that the "empty character string" has *some width*, ie non-empty!

So, when we want to align equal signs, like this:

X = ...  newline
alignl phantom{X} = ... newline

we cannot really use "" in place of alignl.

Therefore, the problem we have is either:
1. The Math Help is misleading and this discrepancy should be written out clearly to users.  And it should stop advise users to use this non-empty string for visual matter.
or
2. The "empty character string" should have no width and the *width* that we see here is a bug.