Well, part of it is how long it stays saturated to the degree that there's no space open for gas exchange; past 20 min. or so, it becomes more damaging... yes, some noob's end up watering the hell out of plant repeatedly, like they're water-boarding the poor things!
... free draining media can shed the water in time, as long as it drains completely away, no back-wicking from a saucer... coco is famous for it's capacity to hold and release water due to it's springy-spongy texture,.. peat is not like this, in fact for my carnivorous bog plants, peat and perlite (and sand) are the medium of choice because it holds water so well,.. these plants literally sit in a shallow pan of water all the time! So peat-heavy mixes should be watered more carefully, and have plenty of perlite...
Watering to 10-20% run-off is usually a wise thing to do, especially if you're using synthetic nutes,... this keeps the salt build-up from getting too bad, and causing all manner of problems... any pot is kinda like a cone coffee filter: as water/nute solution moves down through the media, it increases in conc. of solutes... Organics it's not necessary, unless there's been a big overdose of something! In any case, keeping the pot from getting soggy bottoms or forming dry patches from inconsistent, uneven watering is always an issue... using a wetting agent/water spreader can help a lot with this, particularly with dry patches from media that's become kinda repellent,...
seedlings, it's a bit more tricky. Never let them dry to stress, that makes for stunters from root damage,... too much and you get potential damping off, and again, root damage from smothering; letting it dry a bit at the surface help force the roots to delve deeper, but that's a tricky juggle as a new grower, to learn how fast things dry, in different conditions, what to expect from changes in them, etc,... Personally, I try to keep things as evenly moist top to bottom, with some surface drying (not totally) down a inch or 2 depending on their size,...using a mister can help regulate your surface inputs, and not make the lower levels overly wet from rehydrating that upper layer frequently,...
:smoking: From what I see in Sick Bay, nute burn, bad pH management, and underfeeding are the major issues with noob's,... coco especially! so many think it's just another type of soil, and treat it as such... and end up having problems-- sooner, not later!
Master it though, and you can grow-
!