Find a new dealer. Not every MB dealer has someone that can spell 4matic, let alone service them. MB only imported 400 Es and 400 TEs per year for 4 years so they started with 3200 cars and attrition started at that point. The 4matic system does have a diagnostic module that the HHT can access. Some dealer techs use a digital impulse counter and convert the codes with the manual to tell them what the pulses mean. Either way works, the HHT is easier but it costs more $$$.
If they never checked the diagnostic codes when they told you about the battery problem, they aren't worth going back to tell them they're incompetent. You haven't mentioned exactly what your 4matic problem is, we might be able to help if you offered some details.