writing differences that I noticed

[ololololo]

The only way that would logically be possible is if it is actually a key to a cypher of some kind, or a way to identify the lines themselves.

Or they were very difficult to see, which is why they were outlined
The reason could also be a malfunction of the pen - it could pour ink "quickly", which made the first strokes very bold, while the rest were duller. At least, that's what happened with my iron pen.

But if you consider the time frame of the supposed writing of the document, would that not mean they were using quill-based pens?

There's not much of a difference. 
If anything, I'm not talking about a fountain pen, but an iron pen that needs to be constantly dipped in an inkwell. In other words, its principle of operation is almost the same.