I don’t want to give advice as I am still very new. This research paper has a lot of good information about bottom watering in coco.
A sub-irrigated planter (SIP) is a container irrigation technique in which water is supplied to the crop from the bottom, stored in a saturated media-filled reservoir beneath an unsaturated soil, and then delivered by capillary action to the root zone. The aim of this study was to optimize the...
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According to the paper in a bottom watering/SIP system the top 2 layers (they divided the depth into 5 layers) has a higher concentration of salinity than a top fed system. However, the bottom 3 layers of a SIP system has much lower salinity levels than the top fed system. Greater soil moisture level -> less salinity in coco. Also, taller pots (greater than 15 cm) had a better yield and better distribution of salinity than shorter pots in a SIP system. I do believe they flushed the SIP system at least once in their study - not entirely certain.
I would say your concerns about establishing roots on the top half of the medium is entirely valid if I understood the paper correctly.
Based on those results it makes sense to me to top water initially so that the roots can initially establish themselves in the top half of the pot then switch to bottom watering so roots can seek out the bottom half.
Again, I don’t want to be prescriptive as I am very new to all this.