Walt That seems harder to justify from a fiction standpoint. Also, the size difference between factories seems potentially problematic from a balance perspective. For example, you could theoretically surround a nuke factory with 10 ammo factories for a 250% buff.
What?!? 10 Ammo Factories would cost 100k, for the same cost you could buy another 2 more Nuke Factories, get 450% production (3x nukefacs producing at 150% compared to 1x nukefac + 10 ammo fac producing at 350%) -and- still have 20k left over!
Also, from a lore perspective this entire game obviously operates on a different reality (Walternate Reality) and requires some severe Suspension of Disbelief. Hordes of untiring emotionless robot worker ants crew manually carry jars of energy from the reactors to a room with machinery where they're turned into bullets or missiles or whatnot.
It's way less of a stretch to say (for example) the ammo fac can help the missile fac by producing casing/explosive warhead for it, letting the HE fac focus on missile guidance and propulsion production, etc, and give a smaller adjacency bonus if you felt the full bonus was too much.