While I don't have the game yet, such perks typically work passive in RPGs and will always increase your health by the given percentages, even after you've gained more health.
To explain this with mockup numbers (these don't include any bonuses given by the perk; they're base values):
Scenario 1: Your character has 100 health, obtains a +20% health perk, he gains another 100 health.
Scenario 2: Your character has 100 health, gains another 100 health and then unlocks a +20% health perk.
In the end it won't matter, since the passive perk isn't a static bonus that is applied once. It's a passive effect that is applied overall.
Scenario 1: You start with 100 health. After unlocking the perk, you'll get a 20% bonus, so you'll end up with 120 health. Now, due to the perk, for every 10 health you'd normalle gain, you'll actually get 12 health! So if you collect another 100 health, those will be modified to be effective 120 health. In the end you'll have 240 health.
Scenario 2: You start with 100 health and raise this to 200 health. Now you unlock the perk and get 20 % bonus health: In the end you'll have 240 health.
There are actually only a very few games that apply bonuses in a one-time way similar to what you describe. Those are rare and I can't remember any game out of memories that actually does that. There could be a game where you find a magical chest, that will always include as many coins as you carry - that would be a good example. But as far as passive perks go, those are pretty much always as described above.
Edit: Just remembered an example for such a "wait to get something better" approach - although it doesn't involve health.
In Final Fantasy VIII the loot you'll get off enemies as well as some spell sources throughout the world will change as you level up. The enemies "level" with you, and at given thresholds they'll start to gain new abilities or loot might be replaced. Loot works similar in some instances of the The Elder Scrolls games.
Some games feature treasures that will require you to have a special ability or perk early, since you won't be able to return to that place later on, but I've yet to see any game that punishes you for unlocking some ability or passive early.