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 â€œFFXIV Service Centerâ€ 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.