If you will sli( which I do not recommend) then it is better to buy a full atx motherboard and case.
A M-ATX motherboard has only 4 slots so the two cards will be installed together which is poor for cooling. The top card will run hot.
SLI will win you synthetic fps benchmarks, but
A single great card like a GTX1080ti will game better as a rule. You will avoid issues such as screen tearing, stuttering and non support in some games.