(1) Well - there is an idea that I had a few days ago ...
Since in a different line of conversation you talked about manual operated switches (throwing directly by clicking on the icon) in context of automatic signaling - I thought it would be nice to have switches that only a crew on the ground can control, but still show them and their status on the grid. Everything would be the same except you can't throw or lock them, because they are not remotely controlled. There needs to be something that would instigate the virtual ground crew to throw them. This is also for cases when switches fail to throw (like TD3's switch failure).
(2) If cars are unattended but still present (via split and later merge), the block is occupied. If cars are assumed to be left on the main while the train works somewhere else and you don't want to use the rather cumbersome split/merge (it is schedule based and thus not very flexible to address daily variations), the block can be set to "maintenance blocked". Are you talking about something similar to maintenance on blocks, lets say "protect blocked", with just a different color?
(3) There is something in the works to have "protecting" switches, which are those not traveled by the train for which a route is set, as to prevent loose cars from adjacent tracks to roll into that train.
This is more powerful than just having two switches linked together as TD3 does. As per rules (in some jurisdictions) switches need to be aligned for protection only for regular routes, but not for switching routes. Furthermore, you can set protections if the route you're protecting does not have switches, but there is a crossing with a minor line that has protecting switches - sometimes with the purpose just to derail a conflicting movement instead of running into the main line. Moreover, besides of regular switches, we have also slip switches, single and double, in our inventory, which can make it very complicated. Finally, there may be some requirements to have switches aligned beyond the signal at the route destination - just in case the rails are so slippery that the train runs through the stop signal (won't happen under normal situations and we don't have impacts of the weather included in our simulations - yet).
All of this can be addressed. However, at least for the time being, those protections need to be set case-by-case by the route author to be included in the scene definition file.