Depends on how much of a jerk your DM wants to be.
Technically, by RAW, every target (and it has to be directed at targets, not the area dispel) is affected equally. A DM could rule that the DC difficulty goes up by 4. Or if he really wanted to be nasty, he could rules that every secondary gains a reflex save. That's not how it reads, but hey, I've read a wide number of viewpoints on the matter. You'd be surprised.
The main issue is this: Area dispel targets everything for 20'. Chain Spell is +3 level adjustment and only goes out to 30' and needs to target specific objects. Do you really need that 10'? How about Widen for +3, that will get you 40' and be the same level. A widen metamagic rod is far cheaper. I suppose you don't want to target your allies, but you roll seperately for each thing you are dispelling. This is my judgement call, but I don't see any reason why you can't choose to fail your roll against your allies. If your DM sees it the same was as I do, then chain spell is pointless on a Dispel Magic.