Flat fee upgrade has been gone for more than a year already. That is correct.
However asking $100 a day for a BMW 3 is ridiculous, this thing's reasonable upcharge indeed should be no more than $25-35, but the agent basically decide what price to charge themselves unless there's specific instructions (usually minimum, or what car can't be used for upgrade) from the location.
Not sure about the Tesla's upgrade charges as I've never really asked for one, but $250 sounds more than ridiculous too, I'm sure you can reserve this car for no more than $100 a day in most cases