This is a quick guide to nutrient availability in soil based upon pH.
http://www.avocadosource.com/tools/fertcalc_files/pH_file/pH.jpg
If you are going to use the ebb and flow system I would highly recommend using the clay pebbles in the buckets. The flooding from the bottom may push the coco up and possibly out the top of the pot, at least that would be my concern; but I don't know for a fact that will occur. I do also like the high availability of O2 when using the clay pebbles in the buckets.
And to address your question about coco and if its inert, it is not and it will effect the pH of your water. Right out of the bag the coco may in fact be holding onto excess salts, which do flush out rather easily. However potassium is typically high in coco, thus most coco specific nutrients lower the amount of potassium in their mixtures. Coco also tends to be a sponge for calcium, which can get locked up into the coco where it is difficult for the plants to access it. Therefore typically additional calcium is needed when growing in coco.
Part of what makes this all occur as it does is the cation exchange capacity (CEC), which is relatively low. This means that coco can hold onto most nutrients until something else comes along to take its place. So nutrients always have to be applied when watering coco otherwise the plants go hungry rather fast. This is also the mechanism the ultimately accounts for our pH necessities in coco.