How do PLA, PETG, TPU, ABS and/or nylon work together in a single print?
The answers are   


yes
yes
probably


Which is to say, if you only want to use MaterialNumberTwo for disposable supports, then you should be fine. Presumably the slicer software is material-aware and adjusts the feed so the layer heights are the same for both materials. BUTbe careful that the support material isn't higher-temp than the object material, or supports which start from the object rather than the bed may cause local melting or distortion when the first layer is deposited on the cooler-melt material. 

But if you want to try to intertwine two materials for the final product, then certainly bonding will be a major risk, as will shrinkage during cooling (not to mention the risk of melting the lower-temp material while depositing the higher-temp material on top of it!).  If at all possible I'd recommend printing such parts separately and fitting them together post-print.