You could just write a plugin to change the layout to single for you when it loads:

import sublime
import sublime_plugin

def plugin_loaded():
    sublime.active_window().run_command('set_layout', {"cells": [[0, 0, 1, 1]], "cols": [0.0, 1.0], "rows": [0.0, 1.0]})

Thanks Keith! I've never written a plugin before, but I just tried your example and it worked. My only issue with it is that ST3 opens to the split layout, then executes the plugin and resets the layout. There is a noticeable delay during which the split layout is still visible. Minor, I know. I'm still curious if hot_exit not resetting the window layout is a bug or intended behavior.

I would guess that it is intended, simply because the workflow for deliberately, permanently changing the layout with hot_exit disabled would be cumbersome if ST reset the layout to single mode each time it was closed completely.

The same thing annoys me even with hot_exit enabled - I just have to remember to close the settings window first ;) related: #1402

Guess I will try to remember to close the settings window first :)

I also experienced some layout issues with hot_exit:false.

1. If 2 column layout is active, when closeing Sublime Text the right panel keeps black on the next start.
   
   One needs to click into the 2nd column view to trigger a repaint. This issue exists as long as I use Sublime Text 3.
2. Sometimes the 2nd column even automatically closes without any reason after a second or two, just as I had keith-hall's suggested plugin from above installed, but I do not have.
3. Considder Sublime Text showing only one window with SubliMerge comparing 2 files. Close Sublime Text and reopen it, will also result in 2 column layout with the 2nd black view for a couble of seconds. Than the whole window is closed and recreated with only one empty column. In the meanwhile Sublime Text is unresponsive. All open files are closed, then.

Sublime Text 3126 x64 portable
OS: Windows 10 x64

Fixed in build 4114. The remember_layout setting controls this behavior.