Answer: It sounds like you are doing a great job with your citrus. Keep in mind that Calamondins are especially adaptable to container culture so that may explain part of it. Yellowing overall can indicate low nitrogen, but yellowing at the base usually indicates overwatering or poorly drained soil. Remember that they will use less water indoors -- they are not in the wind, they are not growing as actively, and they are kept on the cool side.
The other factor that might be related to this is that outdoors they are in the rain which provides some nitrogen and also acidity. If your tap water is on the alkaline side you could try using bottled drinking water (not distilled) water. Or you could try a rain barrel to save rainwater to water with in the winter and see if that helps; otherwise maybe consider using a fertilizer for acid loving plants such as Hollytone or even a bit of Ironite occasionally and see if that helps. I know you prefer organic, but for the sake of experimenting you might also try a water soluble fertilizer (with minors) formulated for acid loving plants and see if it makes a difference.
I hope this gives you some ideas.
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