The Beastform Mutagen ability says you can use one ability from alter self...does that include the size modifier effects, or only the things like darkvision?
Only the things like darkvision.
At 3rd level, a beastmorph’s mutagen causes him to take on animalistic features—whether those of an animal, a magical beast, an animal-like humanoid (such as a lizardfolk), or a monstrous humanoid. For example, when the beastmorph uses his mutagen, he may gain a furry muzzle and pointed ears like a werewolf, scaly skin like a lizardfolk or sahuagin, or compound eyes and mandibles like a giant insect. The beastmorph also gains his choice of one of the abilities listed in the alter self spell, which persists as long as the mutagen. He may select a different ability each time he creates a mutagen.
When you cast this spell, you can assume the form of any Small or Medium creature of the humanoid type. If the form you assume has any of the following abilities, you gain the listed ability: darkvision 60 feet, low-light vision, scent, and swim 30 feet.
Small creature: If the form you take is that of a Small humanoid, you gain a +2 size bonus to your Dexterity.
Medium creature: If the form you take is that of a Medium humanoid, you gain a +2 size bonus to your Strength.
The Beastmorph's mutagen does not allow you to actually cast the spell Altar self and the very first line of Altar self says that you only take a new form from casting the spell. Thus you only get the explicitly stated choice of an ability from the list of abilities that altar self grants.