absolutely. If roots are restricted, it will be a smaller plant all other factors remaining the saem -- much easier to see with clones to eliminate fog of war that is genetic variety.
some methods will be more eacerbated by this effect than others, e.g. soil grows will be smaller in smaller pots than the same exact genetics in same sized pots of soilless or hydro. A soilless solo cup will have much greater potential than soil solo cup. It more efficiently feeds the plant.
as far as "too late" or too big.. when you pull it out the number of times the roots are wrapped around will inform you quickly if you waited too long. a few loops is no big deal, but if it's a mess, you can gently loosen that up as you put it in and it might help it spread out more efficiently as it colonozies new substrate.
i had a bunch of plants in solo cups for 6 months. they were showing signs of being rootbound, but still reocvered very fast after transplant. You may have a short transition period before a previously overgrown plant in a small pot kicks back into gear.