I believe most of the 2 cell Li-Ion chargers are not balancing chargers (even the controller chips).  In other words, they use 2 wires, one on the negative end of the pack and one on the positive end of the pack.  The best way to charge a Li-Ion pack is with a balancing charger that uses one wire on the negative end of the pack and a wire for each postive terminal in the pack.  For two cells that would be three wires.  There's no major issue with using a 2 wire charger that precludes it, but there is the potential for unbalanced charging.  If one cell wears fast than the other, the less worn one will get over-charged which damages the cell.  
There are two approaches to builit-in charging for a series mod.  You can build the electronics into the mod or use a dedicated connector that simply connects the pack to a two cell charger, be it 2 wire or 3 wire.
I don't really see that much advantage to building the electronics into the mod.  It's only the difference of using a 9V wall wart or a similarly sized charger.  Like 6 of one, half dozen of the other.  Personally, I'd just use a balancing charger 
like this with a dedicated connector built into the mod.  I haven't actually done that since I've only been building single cell boosters, but that's how I would do it.