Is there some way I could disable continuous spell checking or other settings in the substitutions menu by default?

System Preferences only has an option to disable autocorrect.

defaults write -g CheckSpellingWhileTyping -bool false would be overridden by keys on the property lists of applications.

This would only apply to applications that have been used before:

#!/bin/bash

for d in $(defaults domains | tr -d ,); do
    osascript -e "app id \"$d\"" > /dev/null 2>&1
    [ $? == 1 ] && continue
    echo $d
    defaults write $d CheckSpellingWhileTyping -bool false
    defaults write $d SmartDashes -bool false
    defaults write $d SmartLinks -bool false
    defaults write $d SmartQuotes -bool false
    defaults write $d SmartCopyPaste -bool false
    defaults write $d TextReplacement -bool false
done