I don't see a problem with this, as long as you can keep the minimum water level for the Anova. You are certainly not going to melt anything. (That's impossible while things are in water, because they cannot get hotter than 100 ºC while there is any water left.)
Maybe sit your container on something insulating, such as a wooden board. Even if there is little circulation around the bag from the bottom, the heat will make it's way through in short order. If in doubt, add a bit of extra cooking time.