Your comments

 This was added in build 2111

This can be done by subtracting the errant caret from the selection, there are some details at

No problem - it would be a lot more obvious what's going on if the defaults were opened read only 

If you place your settings in the User File Settings, then this won't happen.

The defaults are intended as a reference, rather than something that should generally be edited.

This was fixed in 2091.

The SQL grammar file had a degenerate regex that could cause significant slowdowns.

 5000 line files are, in general, handled fine. Check what plugins you have installed - several can cause severe slow downs.

While counter-intuitive, this is working as designed. scroll_past_end is overridden the the OSX defaults (in Default/Base File (OSX).sublime-settings), so changing the regular default settings will have no effect - you need to place the setting in your user settings.

In general, it's better to place all your settings in your user settings, so they're not lost when updating. It's likely the default settings will be read only in the future.
All key bindings are configurable - take a look through the default key bindings from the preferences menu