Yes they should. It's what Relic refers to as asymmetric balance. It's what already set vCoH apart from World in Conflict.
That's one possible way to achieve asymmetric balance, the worst one arguably. Germans having fewer men that kill faster vs soviets who have more men but kill slower is another way. Soviets having superior TD but Germans having superior tanks is another. All asymmetric balance means is that the two factions are different and don't necessarily have 1:1 equivalency on everything. Starcraft has it too between its factions.
Making factions stronger at different phases of the game means automatic balance scaling issues. It guarantees that whomever has the best "late game" faction is more and more powerful in larger game modes where the probability of the match reaching late game approaches 100%. Thus, you can never have a game where the 1v1 and 4v4 are both balanced. To a smaller extent even 2v2s become skewed by this effect, a mode which is still highly competitive. If you balance for 1v1, then 3v3 and 4v4 become the late game faction's bitch. If you balance for larger games, then the early game factions will be OP in 1v1s. Balancing around resource shortages for OKW also has the same problem when combined with OH teammates and cache resource sharing.