Since no one else has replied, I will have "a stab" at an answer.
You are correct in that the installer is initially the same for all versions but this may only apply for the initial SP release.
Trainz Plus has regular quarterly updates so about 3 months from now the first update patch will be released. It will have a new (and different) build number and will, therefore, need a new full installer for those who will be getting Trainz Plus as a new program and not as an update from an earlier release. So it makes sense to start Trainz Plus with its own full version installer right from the start.
My theory - but this has happened before in earlier releases of Trainz Plus.