As a theoretical physicist, yes physics could definitely be subjective between different species. Physics is the way HUMANS describe nature to themselves. I don't doubt that it describes some greater nature outside of us that is invariant, but it is only a description - not the thing itself. Like mathematics it is an anthropocentric conceptualization that has many arbitrary and historically contingent choices in its choice of representation and its chosen objects of study.

How could we ever be certain than another intelligence (whatever that means) would be capable of understanding the intended message? Unless of course we are already starting off with the major assumption that the only things that can be intelligent are things like us. I'm not even sure that intelligent has any meaning aside from denoting behavior "similar to us".

If they could discover the probe at all and view the plaque, lots of things are already very similar.