Technically, the rules imply that dragons can't have level boosted spells, based on the general rule for innate spellcasting and the lack of any exceptions mentioned for the dragon's version of the ability.
I don't like that, but I'd rather stick to the rules on that. Would anyone care to provide a convincing argument to let me allow it without houseruling? (I'd really appreciate it).
I haven't had time to look this up (basically because our new DM has my copy of the DMG, MM, PotA, HotDQ, and RoT books), but the MM is one area where I don't really consider changing monsters to be "house rules".
Monsters have always been guidelines for creatures. DMs can and should go out of their way to change them up once in a while. For example, putting a Troll into the game where its regeneration stops working due to cold, not fire. It's not that the DM is housefuling Trolls in general, it's that he's adding in a new type of creature that does not exist in the MM.
With regard to Dragons when I was DMing, every Dragon got 2x Cha spells (somewhat equally distributed over spell levels to simulate them acquiring new spells as they got older). 5E Dragons without spells are, to me, just big brute lizards. I don't consider this "unfair" or under the label of "house rules", I consider it populating the campaign world with monsters that make sense for me as a DM and which emulates more closely monsters from earlier editions of D&D (Dragons had a ton of spells in earlier editions).
So it's not that "dragons can't have level boosted spells", it's more of a question of "why wouldn't a DM give them level boosted spells?". The game is called Dungeons and Dragons. Dragons should be the epitome of bad asses and not just the "Monster Du Jour" that the PCs beat the crap out of today. Every Dragon fight should be memorable and nail biting at a table, at least IMO.