ATLS will work perfectly, if you place multiple approach triggers (using the 2-direction/4 trigger system).
Set the closer triggers to ignore trains of priority 1, and the distant triggers to activate only for priority 1 trains.
Now, when you are going to park any cars near the crossing, set the priority on that train to 2 or 3. The train will be moving slowly when it approaches the road crossing, so it will still give the crossing time to close before the train arrives.
Assuming that you placed a double set of approach triggers on each side of the crossing (in addition to the two you need for each track right at the crossing to de-activate it), then your train will release the crossing properly before it is parked in the yard.
Make sure that none of the triggers is placed where a train will be stopped. That would foul everything up.
You must remember to set the train priority properly, but I find this much easier than using invisible junctions, and also allows me to set crossings up so that MOW trains do not foul the crossings unnecessarily. I set all of my triggers to ignore priority 3, and set anything I don't want to trip the crossing to 3.
One thing you must make sure of when you use the ATLS system, is that your train must cross all 4 triggers (approach, both exits, and the other approach) before it reverses or stops, else the whole system may act unpredictably for another train.
There is now also a fix for starting a session with trains on the triggers. I'm not sure how to use it yet, but it is available on DLS.
The ATLS system by Boat is by far the best crossing system available.
FW
EDIT: I have set up a small test route with the ATLS crossing set up as I described, with a small yard very close to the crossing. I am getting excellent results with the ATLS V2.5 system. It seems to be handling the stopping and reversing on the crossing much better than with the older version. I am going to continue testing with multiple trains passing while the local is backing into and working the yard.
In my setup, I have a single ended yard, so there is going to be a lot of reversing over the crossing.