The most important part of Lithium Ion batteries is the BMS (Battery Management system) that monitors each cell's state and give's accurate reports of the storage unit's actual capacity!
Compared to Lead batteries which have a nice curve depending on their charge status it is not same for Lithium Ion ones, also a curve used by most current lead charge controllers to replenish a flat battery!
We use Li Ion storage a lot here de to their higher life span (cycles) and efficiency (much much better than lead alternatives), yes you can use a normal lead battery charge controller as long as you are respecting the max cell voltage but then you start saturating the Lithium Ion battery and cause it to wear out fast/fail once it's full and keep pumping in current!
Good read on the subject:
http://batteryuniversity.com/learn/a..._ion_batteries
Though back to initial topic, good to see the use of Li-Ion battery in here, less weight, better lifetime, no real issues of wear when exposed to the same temperatures inside the engine bay as with Lead batteries.