Couple of things, the first being something you can't do anything about but will be good to know for your next grow - your pot is probably too small. Next time, grow in at least a 3 gallon pot.
Secondly, coco requires being wet pretty much all the time so I would suggest you increase the frequency of your waterings/feedings... plants at this stage of the game start drinking a LOT more than they did in veg. When you water, make sure you're getting at least 10-20% runoff... I don't think .25gallon is doing that for you - so up the amount of water she's getting.
Top dressing with more coco is fine, particularly if that's where you're seeing exposed roots.. but don't try to either take the plant out of the pot to add coco to the bottom and definitely do not try to transplant into a larger pot... that will mess up their timing and autoflowers are particularly sensitive to having their timing mucked about with... I honestly wouldn't worry about roots coming out of the bottom of your pot...
Good luck - this grow looks really good and you've done a great job!