Because the challenge rating would have been the same.
If the trap lasted only two rounds, that means it would cause 2d4 twice (4d4 damage), with a minimum of 4 damage, and an average of 10 damage. That damage is much lower than the average for CR 3 traps, and a lot of level 1 characters could survive being hit by that trap, so it would probably be a CR 1 trap, or CR 2 at most for being magical.
However, due to the fact that the trap is magical, the minimum challenge rating would have been 3 anyway. CR 1 is the base, then for being a spell trap, we increase the CR by +1 per spell level on the trap or per 10 damage caused on average by the trap (the second one doubles if the spell causes damage on multiple targets).
There are far more dangerous CR 3 traps if they decided that it would last two rounds, and that wouldn't be so expensive to craft. Like, a floor with saws will cause 2d6+7 (average 14) and hit multiple targets in a 10 feet area.
Comparing both the CR 3 acid arrow trap (6d4) and the CR 3 fireburst statues trap (5d4), you will see that even though the fireburst trap deals less damage (by 1d4, and a low reflex save), it affects a 15-foot cone, so it can potentially affect the entire group of PC's.
Traps do not use the minimum caster level or ability modifier
That is not the only trap that was designed with a caster level higher than the minimum to cast the spell though, as we can see on the Fireburst Statues that uses caster level 5th (CR 3, flaming hands 5d4 damage). While the Burning Hands Trap uses caster level 2nd (CR 2, flaming hands 2d4). A Fireball Trap uses caster level 6th (6d6 damage), as another example.
Taking a second look at the Traps page on the SRD, we see no mention of minimum caster level for traps. So i don't think that's a thing for traps (unlike for magic items), you can use whatever caster level you want, that will simply affect the cost to craft the trap if you are hiring someone to cast the spell for you:
Cost Modifier
+50 gp × caster level × spell level
Unlike magic items aswell, the DC to resist the spell trap effect is also different from the minimum to cast the spell. Normally, for magic items, the DC is 10 + spell level + minimum ability score to cast the spell (ie: 13 int for a firewall). For traps, the DC is based directly on the caster's ability score, so if a wizard with 20 intelligence creates a trap, it will be more dangerous (+1 save DC) than one created by a wizard with 18 intelligence.
Spell Traps: Spell traps produce the spell’s effect. Like all spells, a spell trap that allows a saving throw has a save DC of 10 + spell level + caster’s relevant ability modifier.
Similarly, if a wizard 10 creates his own Fireball Trap, it is far more dangerous than one created by a wizard 6. A fireball cast by a 5th level caster will deal only 5d6 damage (average 17, which rounds to 20, +4 CR), while one cast by a 10th level caster will deal 10d6 damage (average 33, which rounds to 30, + 6 CR). Even though it's a third level spell, the effect could increase the CR by 2 points.
For the Acid Arrow Trap, there was no point in being a CR 2 trap since the spell used is a 2nd level spell (CR +2), which would have the same effects as doubling the damage output of the trap and keep the challenge rating of 3. So, the designer probably tried to obtain the best damage for the challenge rating he was aiming for.
