As long as the physics in your established world are consistent and transmitted to the player in a non-disruptive way, anything you pull that deviates from reality is fair game.
By themselves, upside down trees are off-putting and break the immersion. In many scenarios I've seen in this game they're needless clutter for the sake of it.
Since reality inspires games and a lot of games take hints from reality (even mario games), being put off by something that doesn't make sense is perfectly legitimate. I can't say anything about upside down trees here in this regard but I can throw in a comment about the bush atop the sizrable platforms:
Nintendo's developers know that breaking the logic of what players are used to can easily disrupt the entire experience with a game. Take a look at these examples:
Grass atop the brick structure.
Nothing crazy in terms of cave scenery. The background, in fact, has a similar structure to the cave bg found in SMB3.
More believable cave settings.
On the topic of circumventing this...
an easy approach is by making the environment seem more alien as a whole. If the tree structrues are abstract, the setting of a seperate environment with its own rules is conveyed more easily. Making giving the trees a strange colour and texture can go a long way.
Yes, turtles walking on two legs which can be kicked out of their shells don't make sense in real life. However, wouldn't it be offputting if instead of having their own sprite with its own characteristics they'd be generic turtles? The abstraction through body shape, proportions, colour and shoes makes Koopas make sense in the context of their universe.