Yeah. I often exhort people to design carefully and not take it lightly when it comes to charging devices for Li-ion batteries. And, I'm also often amazed at how many engineers think there is no risk, and are ready to use very inadequate solutions. Li-ion batteries, despite being very common these days, are still unsafe when not treated properly. There is unfortunately no real replacement technology as of yet - at least not at the same cost and with the same capacity to volume ratio. But I for one really wish they were gone for good. Of course when charged and protected properly, they are safe to use, but there's just so much that can go wrong and the chemistry is still inherently unsafe. I wish we switched to something safer (and more environmentally-friendly if possible). Hopefully this will happen. Soon.
A 100% software-based charger would be one of those inadequate solutions. Unless you're very experienced designing software for safety-critical devices and use all the right tools and processes, just don't do that. It's a recipe for disaster. And I don't expect a musical gear company to be experienced designing safety-critical stuff. Just not their area.
Now from the little I got here, we don't know for sure what the problem was. It appears that a firmware update could fix the problem, so that's probably why you (and I, following you) assumed it was a software-only charger. But we don't exactly know 1/ whether the overheating came from the battery or from the charging electronics itself (although, the electronics could overheat but it would have to be very badly designed to have a risk of fire, so assuming the battery is involved is reasonable here...), and 2/ whether they used a dedicated charging IC or not. Supposing they actually used a dedicated charging chip, the problem may also have come from the charging current, that could possibly be programmable and set by the firmware. Of course, if that is the case, allowing a max charging current - on a hardware level - if it's software-programmable, too high to be safe, would be a very bad design decision as well.