This is not what your announcement says.
We are also thrilled to announce the beginning of pre-orders for Battlefleet Gothic: Armada. In order to reward the commitment of players who will support us during the pre-order phase, and those who will join the community during the first couple of months following the game's launch, we decided to offer to these 'early adopters', for free, an additional faction - the Space Marines - which will be available to play a few weeks after launch. This additional faction will be playable in battles played in both Multiplayer modes and in skirmish against the AI. Players who pre-order the game will also receive access to the Multiplayer Beta, that will start a few weeks before the official launch.
There is no mention that it only applies to specific retailers, and beta access and the free factions are both told to be perks for pre-ordering. The news on the Steam Library page repeat the message of that announcement - that preorderers/early adopters will get the free fleets. Considering keys bought from legitimate retailers are indeed Steam keys, they will receive the same news.
Can you confirm GMG-bought Steam keys gain some preorder perks (beta access), but not others (free factions)? If this is the case, your marketing has been very misleading. I think it's clear that that the impression it's been giving is that all preorderers will get these perks, and suddenly pulling that back is frankly terrible PR.