When a small summoner summons a medium Eidolon and fuses with it, what size is the resulting combination?
The eidolon must be at least the same size as the synthesist.
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While there is no rule specifically mentioning a size increase on neither the Synthesist's Eidolon ability, nor the Summoner's Eidolon base ability, when discussing the several FAQ requests about the synthesists, Seak K Reynolds (back then, a Paizo's Developer) did give us an example of what happens when a medium-sized summoner merges with a large-sized eidolon:
I've talked to Jason and updated the FAQ about share spells. To sum up: yes, a regular summoner is able to cast humanoid-only spells on his eidolon (duh); yes, a synthesist can too because it doesn't alter share spells.
There is a bit of weirdness about the synthesist and enlarge person that Jason wants to think about for a bit because of the "eidolon must be at least the same size as the synthesist" rule. Basically, if you're Medium and the eidolon is Medium, should it be assumed that the spell affects you "both," or is it a weird case where the summoner "outgrows" the Medium eidolon. Likewise, if you're Medium and the eidolon is Large, you already have the Large benefits, so turning into a Large summoner inside a Large eidolon-shell shouldn't have any effect.
Anyway, he's going to let that "roll around in the old rock tumbler," as he puts it.