The base price, in this case, expects the scroll is created at the minimum caster level required. Hence 75GP given by (12.5 * 2 * 3)
This is also why scroll costs vary by who scribes them.
You can choose to create a scroll at lower than your total caster level, if you want, or you can use your full caster level to gain greater effects (such as extra magic missiles).
The scroll's caster level is also used for effects such as Spell Resistance and resisting Dispel Magic. If (for whatever) reason the spell refers to the casting stat of the person casting it (for instance a Wizard's Int), the lowest needed to cast the spell is used. (e.g. a 2nd level spell requires 12 in the stat, thus the modifier would be +1)