Well, I'm sure you noticed that actually Blue Rose isn't going to be d20, so it's a bit of a moot point...
But I also think you're confusing d20 with D&D in several of these specific line items you came up with.
"-no ability scores, just ability modifiers"
Not a big deal, since you don't actually use the ability scores for much of anything other than to figure the modifier. Actually keeping the score is a relic from older versions, not a really functional aspect of the system.
"-no character classes."
Mutants & Masterminds already doesn't have classes. Neither does d20 Call of Cthulhu. Although the Heroic Roles sound suspiciously similar in concept to a generic class, so I'm not sure that's really a substantive change anyway.
"-no class abilities, just feats"
Also not really substantive, in my opinion. Class abilities are typically just class-exclusive feats anyway, in practical terms. Or maybe I just have a bad habit of glossing over details and looking at "the big picture." I can't see how this is all that big a deal. A lot of recent d20 alternate core classes (especially thinking of the classes of Midnight and Monte Cook's Arcana Unearthed here) are already between these two extremes with large a la carte class abilities lists to choose from.
"-no hit points"
That's a pretty substantive change, but it was in Mutants and Masterminds already, and is even in an official D&D book already (Unearthed Arcana) so it's not exactly earth-shaking.
"-totally different magic system"
Plenty of d20 games have totally different magic systems. Heck, plenty of D&D settings have totally different magic systems (Rokugan and Sovereign Stone immediately come to mind.) That's a non-issue.
"-no experience points"
d20 Wheel of Time and d20 Call of Cthulhu did this years ago as d20 games, put out by Wizards of the Coast, no less.
"-no miniature based combat"
First edition d20 Star Wars and d20 Call of Cthulhu didn't have Attacks of Opportunity except as an option, and without that, miniature-based combat is hardly a necessity. I wouldn't call this a core aspect of d20, but rather an evolving business strategy specific to D&D, based around selling D&D Minis.
"-different alignment system"
Again, every other d20 game other than D&D has that.
I think most of these changes are certainly not core to d20, and are D&D specific. And the others that are more substantive have already mostly been done anyway.
But to answer your real question, certainly none of those changes on their own come close to making the game "not d20". Even in aggregate, those changes aren't enough to make it not-d20, especially since many of those concepts are not core to d20 anyway.