Lots of battery discussions recently - I like it!
I cannot see any reason why it would be an issue to keep the charger unit itself connected to mains power. Don't hesitate on that one. And, that warning you found is probably there to prevent you from over-discharging. That will damage the cells and will lead to accelerated degradation (reduced capacity when full) at best, and physical damage at worst.
Now, different battery chemistries have radically different characteristics. I'm more familiar with lithium than other types, but even within the lithium family, there's lots of variety.
Typically, lithium batteries do not like extreme temperature + high state of charge + time. Leaving a lithium battery in the charger for a long time isn't the issue directly, it's leaving it at 100% for long periods. The potential capacity degradation the cells will experience is also accelerated significantly by temperature. For many lithium cells, the difference in degradation between 100% and say even 90% is huge. Also, storing at 10C versus 40C is equally huge.
There are also an enormous variety of lithium cells available, all optimized for different things. Higher power, low-degradation, more charge cycles. I don't know what kinds of cells Festool chooses and what tradeoffs they made for their packs. I'll speculate they want higher power.
Unfortunately, I don't think the charger-on-a-timer trick will help much for degradation (if that's your goal). Because, even once off, the battery is still sitting at 100%. And, self-discharge will be very low, so it will sit there at high state of charge for a long time. Of course, you could try to time it so they only end up about 80-90% full.
But, what good is having a battery if you cannot charge it to 100% without damage? Batteries are a consumable, they just take a long time to consume. If you leave your batteries at 100% always, you will lose capacity faster than if you store them at, say 50%. How much? I'd guess not very much, but perhaps others with more experience with Festool batteries can comment. What bothers you more, having to charge mid-work, or having to replace batteries a little sooner.
I try to balance my usage/charging so that when I'm packing everything up none are at 100%. But, I don't over-think it too much, and I don't lose any sleep if I mess up. These kinds of gymnastics might add a little to the useful life, but sometimes you just can't be bothered. And, it is damn annoying to get started on something only to realize your battery's dead.