Mechanically, that's a great way to do it, but I have had some rough experiences weaving that into the world. For example, if I tell the PCs that one of the adventures I've set up has an adult red dragon as a boss (via rumors, etc), then they know what to expect. If they wait to take that guy on until level 20, though, they're over-leveled for that opponent and balance gets trashed, resulting in an unsatisfying fight. Admittedly I'm using a dramatic example here, but I hope y'all get the point I'm making.
I think this can be countered in a few ways:
- Reskinning: Sure, you can always palette-swap that adult red dragon to an ancient red dragon, and probably no one will notice (or be polite enough not to point it out if they do). This feels unsatisfying to me because it basically nullifies the player's choice - they waited specifically so they could trash a bad guy and feel really awesome doing it. If I inflate the bad guy's stats to challenge them, I've just made their choice meaningless.
- Proactive Bad Guys: The PCs don't know if they're at an appropriate level to deal with a bad guy, sure, but you do. Why not just have the bad guys come a-knockin'? If they start doing Bad Guy Stuff in front of the PCs, you're signalling to the PCs that these guys are a problem. And of course, you can always have the Bad Guys come after the PCs' resources and connections, too.
- Smart Bad Guys: Otherwise known as the Tucker's Kobolds approach. Assume the bad guys have connections, resources, and networks of their own. They've been hearing about the PCs' exploits, and have taken countermeasures. That adult red dragon? Well, it's now hiring mercenaries to set ambushes between its lair and the PCs base, or launching full-scale attacks on the PCs' allies. Or maybe it's started lending the PCs' allies money, with some very onerous terms and conditions (like coming it the dragon's aid if it's attacked). It never faces the PCs in its own lair, either, breaking up its hoard and spreading it around to multiple lairs, each with layers of traps and defenses to slow the PCs down, not to mention false entrances, false lairs, etc. It no longer uses basic poison, it uses wyvern venom.
Just my two cents.