I disagree on two points; first, I don't think intention matters in whether something is balanced or not (otherwise 3.5's Toughness would totally be a balanced choice), and second, balance is actually better defined as "equal power, equal cost": that is, there is some sort of fair cost for everything, and it is proportional to the effectiveness of the option. Whether that cost is character points, XP, levels, feats, magic item slots, gp, spell slots, or something more exotic is not important; the important thing is that there is a fair exchange rate. (This is complicated extraordinarily by the use of multiple exchange rates in the same system, such as levels, feats, magic item slots, gp, spells, and so forth, with inefficient conversions between.)
Importantly, balance does not rely on equality of options; instead, it relies on more effective options costing more, in some meaningful sense.
And, as I previously stated, perfect costing is not only extremely difficult, it's not very fun for players who enjoy optimizing. Therefore, a certain proportion of "discounted options" is reasonable. (Just like in life, where it's possible to buy groceries with nothing but coupons if you spend enough time optimizing them.) Imbalance becomes problematic, however, when there is an enormous difference in resulting effectiveness; consider a family that rose to wealth and influence by clipping coupons, and how absurd that would be.
That's a matter of preference, I believe; I don't know of any solid line of reasoning why one or the other style is always strictly superior.