This is true, the balance in power from the base class vs. the subclass is different for different classes. So a second subclass would vary a lot in power depending on which class it was for. And yes, for as much as the ranger is derided, I am starting to notice just how strong its subclasses are. Still, if you're restricted only to features up to 3rd level (e.g. via a feat), then that shouldn't make as much of a difference. It's the subclass in its entirety that becomes unbalanced, not so much those earliest features.
Also, the mix'n'match options don't have this issue, since you still only have one subclass, you just pick and choose which features.
This is kind of the problem with doubling up on an entire class. If I were to implement this, things wouldn't stack, so no extra uses of Second Wind or Action Surge (!) or anything like that. You might be able to choose an extra fighting style, or pick up another Expertise (on rogue or bard), etc., but I could also see nixing all base class features. In that case, you have a lot of dead levels just to get to the subclass features. It might make sense to skip straight past all those dead levels, and jump straight to the levels at which you gain class features. If you're spending epic boons for extra class levels, then this is basically the same as spending epic boons for subclass features.