These are not the same. A matter of preference specifically indicates that which you prefer. A matter of choice may mean that depending on the situation or your mood, you make a choice, no matter what your preference. Example: Tom prefers chocolate over other flavors. On Tuesday, there was a "buy one, get one free" sale on vanilla donuts. He chose vanilla donuts on Tuesday, although those are not the donuts he prefers. In this case, if it was a matter of preference, he would have purchased the chocolate donuts regardless of the sale. On Tuesday, it was a matter of choice. He made a choice, even though it was not based on preference. (Really hoping this makes sense!!)

This needs more context. On their own the two phrases don't really mean much. e.g. "It's just a matter of time before this ends badly." provides more context.