Last things first

. There should be a toggle (under tools menu, I think) for Navigation symbols. This will turn off the yellow discs in Driver, but will also turn off other Nav points such as turnout, stop, couple here, etc. that you might want in your session. A more permanent solution is in Surveyor. You need to add the Interlocking Tower Configure Path rule and set all paths for all ITs to disable automatic path assignment for both player and AI trains. That may or may not be desirable since you will then have to allocate all paths via triggered rules (player) or driver commands (AI).
So to your main query, and I should make clear that I am only going by what I have experienced or picked up from others far more knowledgeable than I am. Assuming that your test set up has the IT making automatic path assignments, you need to supply one or more 'anchor' points to get the right path selection for any AI train that approaches the IT section. To my knowledge, Autodrive will merely try to follow the path set in front of it which, in the absence of any other navigation marks, will likely be the 'Priority 1' path in the IT.
In your example, try placing a track mark after the loop. Then issue a driver command 'Navigate to track mark'. The IT should allocate the siding path, since the main line is occupied. However, there is a chance this may not work if the stationary train was placed there at the start of the session (linked to your second observation). I recall some discussion a while ago regarding the ability to un-couple from / couple to consists within IT paths; it may well be that a hitherto undriven train is considered as a consist that would not block access to its associated path. The easy way to test this would be to have the first train drive to a track mark / station on the main line, before commanding the second train to navigate to the track mark beyond the loop.
Finally, take a look at pguy's new MissionControl Manager (there's a thread on the Freeware Announcements forum). Although I have not yet tried it, MCM looks to give you the option of giving AI drivers alternate paths to follow, in case the primary path is blocked, and would seem to be a good solution for passing loops.
Hope this helps.
John