You've extended the phrase "platform agnostic" (a computing term) beyond its boundaries. In the case of platform-agnostic software, it's not so much that the software doesn't care about the host operating system or the underlying architecture, but that it can remain blissfully unaware of it. There is another system (for instance, the Java virtual machine) abstracting away all of the program's access to the hardware and so forth, so the program does not have to "believe in" any particular platform or know the true nature of it if one exists. The program, then, is analogous to an agnostic to whom the world would look just about the way it does right now whether or not there is a God.
The applesauce in your first example likely does need to "believe" in the existence of apples -- otherwise it's just a sauce.
Addendum:
(For some reason I can't add a comment today -- did the whole flushing of cache thing, but still no Ajaxy goodness.)
The question presupposes the existence of a single word that can be dropped into the place vacated by the deletion of "agnostic". There is no single English word in common usage that can fulfill that role, since this particular usage of the word "agnostic" was introduced into the language in a fully grammaticalized form at its coinage. Within the tiny world of computer programmers, it makes a degree of sense (even if it is wrong), but it takes the place of several entire phrases.
The word "indifferent" has been proposed, but denotation is not enough. A century or more back in time it might have made sense, but "indifferent" has since taken on a connotation of "apathy" rather than "universality" or "inclusive". There are other single words that have a similar meaning in limited technical realms, like "non-specific", but they don't fit into a more general context and are as likely to be misinterpreted as "indifferent".
