Isn't this a variation of the Oberoni fallacy? "Characters are dependent on magic items" is the proposed problem and "use appropriate(lower level) challenges" is the rule 0 reason it isn't a problem.
Only if you think that you need a houserule to allow PCs to encounter challenges of different levels, or for a DM to adjust the challenges he puts in his game based on the PCs in the party. It's really no different from a DM (in 3e) putting no traps in a dungeon if there are no rogues in the party or having too many encounters with undead, constructs and elementals if there are.
The only reason this has not been an issue in 2e and earlier editions is that the rules provided only vague guidelines for what was an appropriate challenge. If the DM was designing an adventure for a party of PCs with fewer or less powerful magic items, he should pick less powerful monsters. Alternatively (for more sandbox games), the players were expected to exercise some judgement and avoid fights with monsters that they were not equipped to handle.
Common understanding holds "magic item dependance" to refer to the tendency of the 3.X and 4e editions of D&D to inadvertently use the growing bonuses of magical items as a major determining factor in a character's ability to succeed against equal level challenges.
I would argue that it isn't "inadvertent", though. I'm fairly sure that the intention in 3e, which was further refined in 4e, was that the PCs in a typical game would be on the receiving end of a stream of gradually more powerful magic items. Based on this assumption, you could get an idea of what a "typical" party would be capable of, and hence, the power of the monsters they would normally be able to defeat.
You could take the other approach and assume that PCs don't ever get magic items. However, if monsters are "balanced" on this assumption, then DMs who do hand out magic items will find that equal-level challenges become cakewalks for his PCs. You then need to put in guidelines to tell the DM that if the PCs have such-and-such a level of power from their magic items, they should be considered so many levels higher than their actual level for the purpose of determining what would be a "normally" challenging encounter. It really boils down to the same thing in terms of math, as mentioned, no different from using THAC0 vs BAB or saving throw modifiers vs static non-AC defenses.
If there was an error made by the design team, (IMO) in was in assuming that the "steady stream of magic items" playstyle would be more popular than the others, and in not giving guidelines for how to run games and estimate what would be a good challenge if the wealth by level guidelines (or whatever) were not followed.
In 4e, where characters are expected to have a +1 magic item bonus per 5/levels to hit, damage, ac and defenses, at level 25 a character will hit at least 2 times more often and be hit at least 2/3 less often if he is equipped with level appropriate magic items than if he was using non-magical gear.
So we're talking about the PCs having attacks and defenses about 5 points lower than they would normally be expected to have? Just send them against monsters 5 levels lower than they are. As mentioned, it's really easy in 4e.
Also "Inherent Bonuses" are not a lack of magical item bonuses. They are just a relocation and refluffing of those bonuses.
Call them what you want, but if you want to run appropriately challenging encounters and don't want to bother with subtraction, they do the job with minimum fuss.