The short answer to your question is YES. The extra acid in the ingredients will hamper the second act of the double acting baking powder. The acids are timed/staged for reaction not the baking soda.
The Magic Baking Powder (happens to be in our kitchen, too) is mostly a single acting formula since monocalcium-phosphate is a low temperature acid (with apparently some double acting properties due to generation intermediate step of dicalcium phosphate; per your link). High temperature acid for second acts typically include sodium aluminium sulfate, sodium aluminum phosphate and sodium acid pyrophosphate.
You can try to counteract that by adding a bit of baking soda, but you run the risk of altering the taste and not having it all neuralized.
If you really want to get pedantic, use a pH meter to measure the acidity of your dough. I suspect tasting the dough might give an indication as well. (bitter alkaline, sour acidic)
Another test might be to mix your acidic ingredients in a bowl with some water and start adding measured baking soda until you see no more reaction (bubbles) and use that as a your basic of neutralizing your dough.
All said and done, I agree with SAJ14SAJ that you'll be just fine going with the existing recipe. There should be enough baking soda left to get something out of your double act. I also heard it from a world-class baker that most recipes can be done with only baking soda, let alone baking powder or double acting ones.
The main problem with adding the baking powder last would be getting it evenly incorporated throughout the dough or batter.
In the traditional methods where it is in the dry ingredients, it can be sifted or whisked evenly throughout the dry mixture which facilitates having it evenly distributed in the final batter.
If you tried adding the powder to a batter that was prepared except for it, even sprinkling it across the surface, it would be more difficult to evenly distribute throughout the entire batter. Also, you would then have to mix or beat the batter again to distribute the baking powder, which would develop additional gluten and lead to a tougher end product.
Remember, baking powder requires liquid in order to react (in dry form, the acid and sodium bicarbonate don't interact with each other). When you think about it, in the major baking methods where baking powder is used, the baking powder is activated as late as possible right before baking—the wet and dry parts of the batter don't meet up until the last step:
Muffin method. The wet and dry ingredients are mixed separately, and can be held. They are combined, mixed gently, then portioned into molds or pans and baked immediately.
Creaming method, common for cakes. Typically, the ingredients will be divided into the three groups: an emulsification of creamed butter and sugar, eggs, and perhaps vanilla; a liquid ingredient or mixture (such as sour cream or milk), and the dry flour mixture. Each of these stages again can be set up in advance. They are combined (usually alternating the liquid and dry in two or three stages to maintain the butter/liquid emulsion and to minimize lumping) as the last step in developing the batter.
So even if you need to try to fit baking in with other preparations, you can stage your prep, up to the final combination at your leisure.
If I want muffins for a brunch party (or cornbread on Thanksgiving, when my oven is scheduled down to the minute), I prepare a wet mix and a dry mix the night before (remember, wet mix in the fridge for safety). When I am ready to bake, I just mix the two together, scoop into the muffin tins, and bake.
Best Answer
If the recipe calls for both (and it's a good recipe), it actually needs both. A common reason is that the baking powder provides leavening and the baking soda helps neutralize a bit of the acid.
It's a little surprising you're finding that baking soda ruins the taste and not baking powder; baking powder contains baking soda. I wonder if "ruins the taste" is an exaggeration or if you had a bad experience with baking soda and are a little more sensitive to it now. But if it's really ruining the taste, it's just a bad recipe. There are a couple possibilities: