Its important to note that the trait "Metamagic Master" does not exist anywhere in Pathfinder material. Its called Wayang Spellhunter in Pathfinder material. The d20pfsrd had it listed as Metamagic Master because they were asked to remove anything specific to the Golarion setting from the site, so they renamed Wayang Spellhunter to Metamagic Master. Archives of Nethys are now the official Paizo srd, and is permitted to use Golarion-specific names and information.
In a few different places I found people saying it was permitted for them in PFS, or that Paizo had an official ruling stating it was allowed, but no link or anything so I can't be sure. There is an entry in the FAQ about Magical Lineage, and it says the trait cannot reduce a spell below its original level. As mentioned, the Archives of Nethys are Paizo's official SRD, and on the site it notes which traits are PFS approved. Both Magical Lineage and Wayang Spellhunter have the stamp of approval (hover over the round icon to the left of the trait name and it reads "PFS Legal").
Furthermore, I'm reasonably confident this combination isn't the threat it seems. In both cases, you are limited to a specific spell, and both are contingent on using a metamagic feat, which you have to spend feats on. Now you are in the hole two traits and a feat just to get this setup. Sure, you could sling Magic Missiles all day long, but you've spent all that to spam one not especially powerful spell. Casting an intensified Fireball at 2nd level would be alright, I guess, but only useful once you are over level 10, and again, spending a pair of talents plus a feat (and not an especially useful feat in general) to buff just that one spell and not even get a payoff till level 11 is not really a threat to game balance. Other examples I've found of this combination seem similarly gimmicky and not really game-breaking.
In the absence of any ruling otherwise and with both traits officially approved, I think you are in the clear.