It really comes down to "ask first". It is not your right to park overnight in any parking lot. Whatever their reason: town ordinance, store policy, manager preference, etc.; they have the right to tell you no.
And those things can change pretty much overnight. So just because you stayed once doesn't mean you can stay again. A problem with an RVer one night can cause a store to change its policy. An ordinance can come into effect between your trip out and your trip back.
As for the idea of identifying RV friendly places like hobos used to do, that won't work well. Those identifications are considered graffiti and vandalism nowadays and would make RVs less welcome than they are now.
While convenient overnight stays are desireable for us RVers, we need to consider all the other people affected by it. And despite the belief that RVers are all wonderful people and never cause trouble, there are a lot of RVers out there who are not considerate, thoughtful or polite. Those RVers are often the ones at fault for stores banning RV overnighting.