We currently think we know what the registry entry in question is used for, and we are probably right. But we do not truely know it, and we certainly do not know how it may be used in the future.
For example, Totem could decide to split the Data folder into separate parts each with its own folder and each pointed to by a separate registry entry - perhaps Cards, Scenes, MiscData and Temp.
It's also an eventuality which could happen, a chasm hole to open in the ground while we are walking in our city and eat us... but the risk is so low that we usually can walk outside without not even thinking about it.
Same about registry changes we are talking about. Anyway, even in such an improbable case, a simple deletion of the changed value and a new installation could easily solve the issue.
Consider a hypothetical program that is identical to iStripper in every way except that the protection against using cards copied from another user is controlled by a registry entry that comprises a 128 bit key made up by concatenating the user id with an encryption key and that by replacing the encryption key part with one copied from a different user would allow you to play copies of that user's cards. Now this is a very weak protection scheme but the fact that it can be overcome by exactly the same mechanism as that used to change the data path does not mean that it would be, in your own words, "intended by the design of the application to be available and used when needed."
Such an extreme case is totally different from the sort of registry changes this thread is about, since the speculated inserted code copied from another user's one would mean acquiring and using stolen and false informations. Which would be, of course, a totally different matter from what an ordinary change of a registry value is.