They aren't illegally entering the car, they're putting chalk on the outside of it.
Yes, without permission, dumping on someone's property is a trespass.
> So to would leaving a hand print on someone's car if you happened to touch it.
It is a trespass, yes. Probably not on its own an actionable one (or at least not one worth civil action) because of the lack of harm, but whether a trespass would be actionable or worth action as tort is irrelevant in the case where you are looking at a Fourth Amendment violation where any trespass by givernment for gathering information to be used against a person (as a violation of legal property rights) is, ipso facto, a violation of an expectation of privacy, triggering the requirements associated with a search.
The legal issue isn't that it is like a GPS tracker, it is that it is a physical trespass (a fairly well-defined legal concept) for the purpose of establishing information to be used against you by the government.
Now, this is also a feature of the GPS tracker case, but it's not the comparison back to the GPS tracker case that is the main issue, but the same underlying principles that have governed the GPS tracker case and a wide range of others.