You are correct that some companies claim that using other battery brands is not recommended with their chargers, and visa versa. I also think it's marketing.
I used Energizers for the last few years until some started crapping out, and recently replaced everything with Duracell 2650s, which I love because they have a lot more capacity than the Energizer 2500s I was using. I passed on buying another quick charger, because right on the back of the label for the Duracell 15 min charger, it said that charging times would vary based on capacity and brand of battery, meaning Duracell is right there giving only that as a disclaimer for using a different battery brand. I have been using these Duracells with my Energizer 1 hour charger without any problem, although I may still buy a Duracell 15 min one just for the increased charging speed. Bottom line, don't worry about mixing brands of chargers and batteries. As long as the charger is made for NiMH batteries, any brand of NiMH battery will work.