With a physical member with intermittent joints (i.e. "just add joints to physical members) you really have essentially one member with multiple joints. The program combines the solution and reports all the individual members as one member.
This physical member concept is used for cases where you might have a long member with intermittent connected joints and yet want that long member to be dealt with as one entity - similar to the top chord of a long truss where you want the whole top chord to be treated by RISA as a single member, yet there are occasional joints and connecting members that affect the matrix solution.
If you "actually split physical members" you are breaking the one single member in to multiple two-joint members.
In either case, the results should be the same in terms of the matrix solution (Josh can you confirm?).
Why you are getting different "results" may be that the results are design results that are affected by the program's perceived design parameters such as unbraced length, etc.