The difference between start/stop-fwd/rev and fwd-stop-rev has to do with a combination of the programming of the inputs and the way the switch works. As you mentioned the rotary switch is essentially a SPDT switch, where only one side or the other can be connected at a time. From your new diagram you have either input S1 OR S2. This would allow you to use F06=000 per page 28.
If you used two separate SPST switches, one for start/stop and one for fwd/rev, then F06=001 would apply. To run fwd, close S1 and open S2. To run reverse, close S1 AND close S2. Therein lies the problem with using the SPDT switch (or the 3pos rotary you have). You can't close both S1 and S2 at the same time, so you can not issue the start input and the reverse input at the same time. Using the 3pos rotary switch would allow you three options: (1) start fwd, (2) stop fwd, and (3) stop reverse (S1 closed/S2 open, S1 and S2 open, S1 open/S2 closed).