If the difficulty of thieving was increased (in a more interesting way than just increasing the DCs) and/or a reputation system was implemented, then BG3 wouldn't have to rely on this "merchant immediately accuses the players of stealing, even if said merchant has no way of knowing who the culprit is" mechanic.
Invisibility should persist while stealing. This would work well the implementation of some type of perceptive radii instead of just a sight cone - invisibility would as per the rules give the enemy Disadvantage to notice you while you're within that perceptive circle.
