I think that the question of whether or not a floor exists absolutely matters to the OP's question. That the calculation only happens during the act of adding a metamagic feat doesn't change the fact that the existence of a floor creates two very different equations for calculating the spell's final level.
Using the original example, with no floor:
(0 - 1) + 1 = 0 (which would have the effect of unlimited metamagiced uses of the spell)
With a floor:
Max(0-1, 0) + 1 = 1 (which negates the effect of Magical Lineage for 0-level) spells.
I'm personally of the belief that a floor is intentional, but I didn't write the rules. I'd rule for the floor, personally, but that doesn't help answer for PFS.