From everything I've seen, the answer is yes, they are the same scale. It appears that the only difference is that the minis provided in Recon are resin as opposed to metal.
The other difference between Recon and buying a faction box is that you only receive 5 characters as opposed to 6 you get in the box set. Not a huge difference though.
Actually, from the looks of it, you're not buying 1 faction, you're really getting 2 factions in the main 2 games they are featuring in the kickstarters. The additional story packs look to be single faction.