Well, it's not entirely clear either, even if you're playing different factions: you grind a couple dozen of your level 6 units, your opponent has the same opportunity — what's the problem? That someone did it faster — that's already a skill, learn to play.
Say, in the game Samurai(Bog)-Term(Inferno) at the starting respawn there was an Inferno-Griffin Conservatory tier 3. Samurai fought it on the bog, meaning he had a territory bonus. Term would have had to fight it on lava, meaning no territory bonus.
The second issue is that some level 6-7 units are universally useful, while others are completely useless. Say, when playing Castle-Necro, the first player absolutely needs to convert skeletons, while the second can just take angels.
And the third is what Lebron described. It's clear that getting burned once is enough to quickly remember this feature, but it still scratches at the aesthetics.
Removing native player troops from the Griffin Conservatory-Dragon Fly Hive (you'll be able to order them, they just won't be there from the start) will make spawns more symmetrical, simplify both the scripts and the understanding of the rules.