if you have gnats, consider different source for the substrate... if stored outside, you get gnats. buy a product with Bti in it, like mosquito bits for a top dress or mosquito dunks if you have a reservoir (not good for irrigation plumbing though). i only mention cuse i see the sticky traps.. can use bti pre-emptively and avoid 99.9% of it.. if i see zero gnats i'll stop using it at some point in the grow, but will use it to stat every time. it's cheap enough and worth it. you'll see 1 or 2 around if the larva is present in the substrate.. it's never 100% but it most definitely controls it - if used midstream it'll corral a problem within 2-3 weeks. sticky traps still good to put out... kill in 2 parts of life cycle that way.
no worries on adding more to the top.. you can easily bury with transplant, too. Roots will lose their function over time due to exposure to light. burying them will eventually cause them to re-differentiate yet again into roots... cause and effect. it's small potatoes either way as long as they are in an appropriately sized pot, which they are.
watering habits will help the most to avoid superficial roots. You are in coco/perlite, so it's easy as pie... find a well-balance nute mix and use a concentration somewhre around 1.3-1.5EC every irrigation with 10% runoff. the runoff ensures each time the concentration is where you want it.
you may need to tweak balance of the various nutrients invovled, but the concentration range will be damn close to what you want relative to your garden's variables. you can push higher and some plants may want a little less, but those contexts are extremely obvious and slow enough to react to with no harm.
change formula? give a little extra runoff and that new balance is in effect immediately... another benefit of soilless grows.
start tracking how much of each nute you feed... ppms, weighted average of label %'s.. whatver floats your boat. when you se tox symtpoms, make note of what levels you are seeing it... if you see a consistent result in this regard, you can easily avoid it in future. Even if i change products, i can devise a formula that comes out near what i used before and be confident it's going to work well, because reality is deterministic and works on cause and effect. makes you feel all warm inside... despite the fact it also means free will may be an illusion, but that's not a topic for discussion here...
:P