Riot does seem to bend backwards for mana champs in their itemization offerings.
Just look at RoA and Rylai's - the best health+AP item for mana-using and manaless champs: RoA has 100 more health and 20 more AP than Rylai's for 200 less gold. And, oh yea, it just so happens to effectively make that champion manaless.
Now, in a vacuum, this is where you say "but what about Rylai's slow?" However, when you look at the difference between your typical manaless and mana-using kit, you'll realize manaless champs are usually given much less utility (read: hard CC) than their mana-using alternatives. So, once each type of champ finishes building their AP+Health item, they're both effectively manaless, but the mana user has hard CC while the manaless champ usually has only slows.
Lastly, the same is true of the other itemization in the game: manaless champs' greatest strength (the ability to skip a stat in their itemization) is neutered by a lack of decent manaless items. Want CDR? You're either building full defense (kindle items) or you have to spend on mana/mana regen (glacial/idol). Want a meaningful lifesteal analogue? Too bad, spell vamp currently sucks unless you're Vlad. Just want sheer AP? The highest AP items are mana items too.
PS: Yea, this is discussing AP champs, but IBG and Muramana are the same argument for AD champs.