My campaign is already using automatic bonus progression rules and I'm interested in how they interact with spells like greater magic weapon or magic vestments. If a character casts greater magic weapon at the start of the day, can the enhancement bonuses from the spell go first, then have the bonuses from the character level go to weapon abilities? For example, if you're at 9th level, could you make your mace +2 enhancement bonus from the spell then make it a +2 flaming, shocking mace with the automatic weapon bonus?
Automatic bonus progression (ABP) aims to emulate some magic items. So I'd say the ABP enhancement should act like normal enhancement on a weapon: It counts first, before greater magic weapon and similar effects.
To stick with the example, you can still get a +1 flaming mace from ABP, then augment it to +2 flaming with the spell. So the combination allows you to choose special abilities in a very flexible way, while the spell roughly offers the same pure enhancement progression as ABP would.
It matters less on high levels - you still lose only a single "enhancement point" to make the weapon magical. And with ABP's legendary gifts, you could hit the cap of +10 before level 20.
EDIT: Hrm, there is still the issue of damage reduction. Given ABP's progression, you probably want to attune two weapons, even if you wield just one at a time: A fancy one, with many different abilities and augmented by the spell, and a reliable one, with a high enhancement bonus from ABP.
Since both the spell and APB are enchantment bonuses they do not stack.
Also the attunement bonus does not grant you special abilities on weapons that do not already have them. The way it works is you subtract the weapons enchantment bonus from your attunement bonus and whatever is left over is the enchantment bonus of the weapon. If your attunement bonus is equal or less than that of the weapon it gains no bonus but the special ability still works. The example they use of a 4th level character wielding a vorpal longsord.. The wielder can still use the vorpal ability, but the sword does not have an enchantment bonus.