Can all 3 uses of Metamagic School Focus from Complete Mage be used on the same spell?
No. In general, you can't use a feat like that more than once at one time. The key is that it says "three times per day", which means that you can use the ability three separate times during the day. There are abilities that let you stack their uses further like you're asking about, but those specifically state that.
Also note that when it talks about prepared spellcasters, it says that you can prepare three different spells that are affected by this feat each day, with no mention of allowing the uses to combine.
Yes, the uses can be used simultaneously, on the same spell. The key being:
The reduction comes in when the metamagic feat is applied to the spell, and that can happen several times during one casting.
Overzealous stacking would be to allow it to reduce the spell level adjustment of a single metamagic feat by more than one (applying the feat more than once to a single metamagic feat on a single spell), but that isn't what is suggested here.