The answer is this prefix spelling rule does not apply to suffixes.
The statement prior to this is, adding a prefix to a root word does not change the spelling of the root word. However this prefix spelling rule does not apply to suffixes. When adding a suffix to a root word you change the spelling for example cancelled is a combination of 'cancel' and 'ed' but you add an extra 'l' into the word. This doesn't happen when adding prefixes.