just make sure that while you water a smaller portion of the pot you are getting it wet all the way to the bottom, otherwise the drying pattern trains superficial roots and leads to other problems down the road.
Despite the commonly repeated myth that you should not 'transplant' autoflowers, you absolutely should use size-appropriate pots for your plants. Potting up is not as stressful as a "transplant". A real transplant involved damaging roots and such. What we do when moving a plant to alarger pot is not stressful unless you pull out the "gi joe kung fu grip action" (tm) ... Don't molest the rootball like a catholic priest with a choir boy in a dark secluded room, and you will never shock a plant from potting up.
The benefits are worth it for the easier and proper watering procedure alone. Not to mention it is a more ideal development for the root zone to do so, too.
it's easy for young plants to look good. The mistakes we make having compounded into visible issues, yet... it's 'handling' any imbalance up to a point where it becomes a problem later.
how they look in 2-4 weeks will tell you whether they are truly in good shape today... and so on in perpetuity... rates of change over time.. finding that equilibrium that results in supremely healthy plants of a wide variety of genetics is the goal. observe, adjust, be systematic about evolving.