Is there a rule of thumb for spacing between jet engines?
Placing the engines farther out is mainly done for bending relief in the wing. Given that the Stratolaunch needs to keep its center wing clear of fuselages and engine nacelles, the engines are out enough already. Moving them farther out would create more thrust asymmetry once one engine fails.

Airliners with a central fuselage are different. We have an answer here discussing optimum engine placement. Why they should not be combined in one nacelle is explained here.