I can't find the relevant text, but I think the assumption is that instead of gaining the improved ability, you gain the previous ability in that chain. So when you'd gain greater shield ally, you'd instead gain regular shield ally.
Found it. It's in the ACG and maybe some other later core books
If an archetype replaces a class feature that's part of a series of improvements or additions to the base class's ability (such as a fighter's weapon training or a ranger's favored enemy), the next time the character would gain that ability, it counts as the lower-level ability that was replaced by the archetype. In effect, all abilities in that series are delayed until the next time the class improves that ability. For example, if an archetype replaces a rogue's +2d6 sneak attack bonus at 3rd level, her sneak attack doesn't jump from +1d6 to +3d6 at 5th level—it improves to +2d6 just as if she had finally gained the increase for 3rd level. This adjustment continues at every level at which her sneak attack would improve, until at 19th level she has +9d6 instead of the +10d6 of a standard rogue.
I don't think the undersized mount feat cares what manner of creature you are riding.
