Exclusions do not seem to apply to generated substitutions

You have found a real bug, not a misunderstanding. Exclusions are applied when the recipe is generated and are not being passed through to the substitution call, so the substitution engine does not know about them. Workaround until it is fixed is to regenerate the whole recipe rather than substituting within it, which does respect the list. Thanks for the clear report, two examples in one week is exactly what makes these easy to track down.

Genuinely relieved it is not me. I had started to think the app had opinions about my palate.

Same thing happens with heat level preferences for what it is worth. I have mine set high and substitutions come back milder than the thing they are replacing.