When you buy a package, you get the files for a specific ruleset. So for example the racial bonuses or the category costs wouldn't automatically make sense when switching between versions.
Also, some books are not completely equivalent in their content. RMC Arms Law does not have the same attack tables as RMFRP Arms Law, small as that difference may be.
That is not to say that some content can be used interchangeably. If you buy RMFRP Spell Law, you could install it on the RMC version of ERA and it would work seamlessly, because attack tables, criticals and spells work the same in both systems. You just need to be careful about the individual content and the house rules in play.
Once RMU is released, most likely the books will be offered as different packages in RPGNow. Spells will work in RMC and RMFRP, and off the top of my head I think that Background Options and Criticals would also be compatible cross-system. Professions, races, cultures and attack tables have some significant changes. In order to make them compatible an official conversion would have to be defined, so that I can code it into ERA and avoid weird mismatchs, such as incompatible categories for the most relevant skills (i.e. Body development, maneuvering in armor, ...).
In any case, there is always the possibility of tweaking the configuration files and asking for advanced customization advice, that is what the forum is for!
Does that answer the question?