Settings can be set on a syntax specific basis. It looks like you have Markdown files set to have a specific different color scheme, and in addition the
draw_centered setting is enabled for them specifically, which makes the text center in the display (thus giving you the wide margin).
The more obvious culprit for that is MarkdownEditing, which ships with default settings that override the built in
Markdown.sublime-settings to include a variety of things, not the least of which is a different color scheme and the centering of the display.
As such you could fix the problem by disabling that package or by choosing
Preferences > Settings - Syntax Specific while you have a Markdown file open and manually add in a
color_scheme setting and set
draw_centered to false to make it more like you might expect.