I think you're just confused by the entire thing. Magnezone does not have high HP at all, it's mediocre at best. The reason why its potential HP is in the 300s is because HP is naturally higher than other stats due to a difference in how HP is calculated. For example, look at Magnezone's stats; its Attack is base 70 like its HP is, yet its HP reaches nearly 100 points more. This is an obvious result of this difference between HP and other stats. The formulas can be seen here (credit to Bulbapedia):
Every Pokemon has this different HP mechanic, so in comparison to other Pokemon, Magnezone's HP is bad. Just go look up another Pokemon with higher base HP and see the difference.
So Magnezone does not have high HP, its HP only looks good because that stat is determined differently.