FWIW, LD, if anything, your post might have come off a little too negative, especially since there have been software upgrades over the past 3 years. However, your cautions should be noted by anyone contemplating using planning software, they are not infallible.
I've also used RealTrax because that's what was in the set I bought. I didn't run into a switch motor problem, but I've only used it for basic Christmas layouts. FYI, I have the latest version of RR-Track and it shows the motor and it's placed on the turnout side of the switch by default, However, it can be changed via properties if that placement doesn't work. I don't know what version you used, but it appears that at least the latest version has addressed your concern.
I do share your concerns about RealTrax in general and that's why I'm changing to Atlas or ScaleTrax for the layout I'm about to begin building. Had I done a little research, I would probably not have bought a set with RealTrax and would have simply bought things individually, though I suppose the track didn't really cost me that much since it was part of a set.
I also share your concern about spacing. When I first started using RR-Track, I incorrectly assumed that if it said things would work, they would. I found otherwise very quickly when I posted my first design and folks told me the spacing in my design was too close. Live and learn I guess.