I'm actually in the same position as the OP. The only PS3 CE's left aren't available from the list of participating SE retailers (Amazon, Game Stop, Best Buy, Wal-Mart, SE Store), so that means they don't come with the pre-order bonuses. That is, any CE bought from a different retailer doesn't come with early access, the cait sith minion, or moogle hat. You'll get all the CE items however.
As to the OP's question, I think the Digital CE Upgrade will work with the PS3 version.
From the FFXIV Pricing/Platforms page: http://na.finalfantasyxiv.com/product/
** The Collector's Edition digital upgrade offers customers the ability to upgrade their standard FFXIV account to digital Collector's Edition status via the “FFXIV Service Center” website that is scheduled to be opened at the launch of official service, which then grants the in-game bonus items included with the Collector's Edition. Customers in possession of the Collector's Edition for either version 1.0 or A Realm Reborn will receive these Collector's Edition items without needing to purchase the upgrade.
Since it's an account upgrade, I think it will be applied directly to your FFXIV service account. Meaning it should work with PC or PS3. I'm not 100% sure on this though.
I think I've decided to pre-order the standard edition myself, but I'm still trying to figure out if the digital CE is worth $19.99 without anything physical to show for it.