Ummm.... No.
Magic system is one of the things that is PC-side modular.
PC-side things are all, naturally, able to co-exist unless explicitly banned. They're not going to ban Warlocks in organised play.
You're being far more pessimistic than you have any cause to be.
Just remember who said it, and look at the Runepriest vs the Fighter. The logic is clear.
Just a couple of other notes on this:
1) It is unproven that 'PC-side things can all co-exist'. In fact I find this whole aspect of the modularity concept highly unlikely. Some limited options will probably work OK on different characters. Which exactly ones those are will be highly dependent on what you consider 'works OK'. I'd note that many people here don't even think E-Martial classes work OK. I'm not as picky as that, but I've been around a long time and I've really not seen this mythical disparate yet equal mechanics in a game.
2) Which option is this? You have to realize, the unpopular 'options' simply won't be developed enough to BE really usable. Sure, you can play your AEDU wizard that has all of 40 spells, or you can play your Vancian wizard that has 300. Even if they are hypothetically 'equal' in some theorycraft way, they aren't ACTUALLY equivalent, which is all I care about.
3) Everything but the PCs are going to be using the 'standard' option in any case where you're playing published material. Of course the DM can deal with this, but what is the point of buying a game where you have to homebrew at least half of it to play how you want? It is the wrong game for you at best.
'Modular' is effectively a pipe dream. Of course you can tack 42 different sorts of mechanical options onto any game, label them all 'optional' and have a 'modular' game. That is not at all the same thing as having a game that fully supports a variety of very different play styles. Supporting that is no less work (and no more likely to happen) than putting out 8 different games and supporting them all. WotC doesn't have any interest in supporting more than one RPG now. Show me where there is even a snowball's chance in the nether regions they're going to support even 4 styles of D&D play. They don't even support 4e's version of GW.
And lets suppose for a moment they DID try to support all those different play styles... What is going to happen? They're going to put out 2 modules grand total for each one, and 1 or 2 supplements a year? Do you think that level of support is going to impress the people playing PF right now? Really? Do you need a bridge? It is absurd. WotC guys are not dumb. They understand all of this. I don't doubt for a minute they'll provide some basic modules for "4e style play" and some for "3e style play" but bluntly one of those styles is going to be DOA because that's pretty much the last we'll here of it. If your tastes don't happen to be the ones WotC chooses to cater to, you're going to be pretty much out in the cold and better off playing a different game.