While that may seem like a simple solution, the exceptions are there for a reason:
1: There are some places where TDs want to give a player the option to "forfeit and fold". The delegates defined those situations in 2013 in Rule 39-B.
2: Betting and raising discipline is essential to poker. Allowing players to toss in any size chip in order to call was seen as an invitation to chaos, and hence strongly discouraged in the language of Rule 41 also adopted 2013.
As you note, effectively the tiny-bet will most often be ruled a full call however a couple problems with stating such in the rule are: A) it might be construed as legitimizing the action as equivalent to the other forms of calling, and B) it might appear to contradict the option to forfeit and fold multi-way when facing a raise of the opening bet.
KEY: In practice the decision tree on an underbet would be:
1: Deliberate tiny-chip bet: always a call (effectively), discouraged, penalize repeat incidents
2: Undercall of the opening bet or any bet heads up: always a call
3: Undercall of a raise multi-way: at TDs discretion either a full call or may permit player to forfeit and fold
To address your concern, it would make this decision tree clearer if 39 and 41 were together as 39 and 40. Since 40 is on Action Out of Turn, it could be moved until a later spot with the other erroneous actions such as after Rule 51.