I think the thing that is the big difference is the charging time. I personally use a Maha charger and my batteries charge up in about 2 hours. So .. with my time being valuable to me, why would I possibly wait for 16 hours to charge them in my scanner.
If you have a MAHA charger, you know that it can be used to measure the capacity of a battery.
The batteries that came with my 396XT have a rating of 2250mAh. After charging them in my MAHA charger, I found that the actual capacity closer to 2100mAh.
My next step was to charge the batteries in my 396XT for the default 16 hours, and then read the charge capacity in my MAHA. Once again they showed a full charge of 2100Mah.
Over a period of days I discharged and recharged the batteries inside my 396XT. Each day I changed the charging time of the 396XT. Eventually I discovered that I could charge a set of dead batteries for 6 hours inside the 396XT and the MAHA would show that they were fully charged.
The actual time required may vary for different models and capacities of batteries, but I doubt that any batteries require the default 16 hours.
Personally I prefer charging inside the radio ( even though I have three different external chargers, so obviously saving money isn't the reason).
I find it much more convenient, and as someone said, less likely to cause wear on the battery door, and wear of the metal contacts themselves. It also lets me give the batteries a few short charges each day whenever I am sitting at my desk for a few moments. I also feel that a 6 hour slow charge is better for the batteries than perhaps a 15 minute charge from a fast charger, but I guess if my time was valuable I could sacrifice battery longevity for the faster charge..
It looks like Uniden has put a lot of thought into the design of the 396XT power supply. I tried at least 1/2 dozen 6 volt adapters before I found one that would not give an illegal voltage message. We also know from the OP of this thread that the 396XT is monitoring battery condition as well. I think we can assume that the 396XT will protect itself from any damage.
Rick