I think I get the idea of the indicator, what you are trying to do. But not sure what the indicator is really indicating there, seems it would depend on how true the top slot is (turned over). If it were angled a bit one side to the other you'd scrape that angle in to the ways to compensate. Maybe ought to use a small parallel or gage block to bridge surface variation on the ways, just measuring high and low spots as it is.
Pete, as Richard mentioned, put some bluing dye on the surface plate, see how the part hinges and how the blue gets wiped on to the ways. I think that will tell you better than the indicator.