They could paint penalty boxes (with an X) to give extra clearance.
There is no where to paint them. You need to move the stop lines back. The ones for the right turn bays in Millwoods the hood of your vehicle is like 3 feet from the tracks if you stop with your front wheels at the stop line. They're way too close as @whatchyyc mentioned.
Need updates. Are they running out of random thoughts like some sort of future heavier trainset preparation to explain things?
I have noticed they are running trains way more frequently and closer together as of late. Almost like they are simulating actual service levels or close to it? I haven't driven alongside a train recently to see what speeds they're reaching. The last time I did they weren't even anywhere close to the posted speeds along the tracks though.

The trains are stopping way more than I think they should too - why are they leaving the station to pull up 2 car lengths to clear an intersection and then having to stop for the next traffic signal? They should have these things in sync so that once the train gets a signal it's pretty much good to go into the next station IMHO.
The train’s switching tracks:
I was passing by Bonnie Doon this morning while a train was also heading southbound. The train was definitely running at a normal operational speed. We were side by side just north of the mall. By the time I reached the next station south of Bonnie Doon station, the train was already almost out of sight on the bridge towards Davies station.
Grounding cables and derails installed at the north end of the elevated section again today on the way home - both tracks. Wonder what was going on today they had it closed it down.
I drove by today and it looks like testing taking place between Avonmore and Downtown, and some pier fortifications taking place by the Davies Station.