I think lots of these issues (at least all the ones that are related to altitudes issues) are likely the fairly uncommon situation of EHAM being below 0 altitude. It will likely require some specific treatment so yes, I don't say there's nothing we need to do to fix it but, in general, it would be best if you didn't based your reports over this very peculiar airport.
About the others when there's a "thing that drives through another thing", we explained so many times GSX vehicles are not really aware of each other (in some cases they are, but not always), because doing that would cause an enormous strain on the sim, because each vehicle would need to know the position of the other vehicles. While this might be possibly be done without connecting to the sim, at least for GSX vehicles, it won't solve any case of any possible collision between GSX vehicles and other vehicles in the sim because, how useful would be an avoidance system, if it couldn't avoid anything other than GSX vehicles ?
Sure you don't want them to drive through other AI or other ground vehicles or even your own plane, but to achieve this, we would need to spam the sim with commands know the position of *all* other ground objects at AI planes, with a frequency high enough to allow correction.
And that's just the performance aspect. The other aspect is this will likely introduce a whole new class of bugs, all falling into the "deadlock" category, like deciding who has to yeld to whom, how to solve conflicts and exit from deadlocks. Better having the vehicles driving through each other sometimes, than not having any service, because some vehicle might have been stuck.
And, lots of potential conflicts can usually be solved by editing the vehicles starting positions, something you'd want to do anyway (or wait for somebody to do it and share it) if you want to use a detailed airport, where you really need to have each vehicle individually placed.
