Just a question to clarify, a player and I have come to the decision that any Variant class abilities supersede those of the proposed Archetype.
Is there a rule that states this to be so?
The player or myself can't seem to find any confirmation. To be more specific the player is taking a level in Paladin with the Archetype of Holy Tactician and the variant feature set of the Shining Knight. Where the Holy Tactician loses the Divine Bond at 3rd, and the Shining Knight gains the Divine Bond at 5th.
I'm not 100% on what you mean by variant class abilities as different from archetypes.
But you cannot take 2 archetypes that replace or modify, if ever so gently, the same class features.
In this specific case, holy tactician and shining knight do not work by the rules, since they both replace Aura of Courage. They don't work either because of them both touching Divine Bond, which is where the "modifying" clause comes into play.
From the introduction to archetypes in the APG:
Most of the options presented on the following pages include a host of alternate class features. When a character selects a class, he must choose to use the standard class features found in the Core Rulebook or those listed in one of the archetypes presented here. Each alternate class feature replaces a specific class feature from its parent class. For example, the elemental fist class feature of the monk of the four winds replaces the stunning fist class feature of the monk. When an archetype includes multiple class features, a character must take all of them—often blocking the character from ever gaining certain familiar class features, but replacing them with equally powerful options. All of the other class features found in the core class and not mentioned among the alternate class features remain unchanged and are acquired normally when the character reaches the appropriate level (unless noted otherwise). A character who takes an alternate class feature does not count as having the class feature that was replaced when meeting any requirements or prerequisites.
A character can take more than one archetype and garner additional alternate class features, but none of the alternate class features can replace or alter the same class feature from the core class as another alternate class feature. For example, a paladin could not be both a hospitaler and an undead scourge since they both modify the smite evil class feature and both replace the aura of justice class feature. A paladin could, however, be both an undead scourge and a warrior of the holy light, since none of their new class features replace the same core class feature.
Both Holy Tactician and Shining Knight are archetypes. Where are you getting "Variant class abilities" from? Shining Knight modifies rather than gains Divine Bond. Both archetypes replace Divine Health and Aura of Justice so you couldn't take both anyway.
Edit: Ninja'd
A character can take more than one archetype and garner additional alternate class features, but none of the alternate class features can replace or alter the same class feature from the core class as another alternate class feature.