There are all sorts of situations in which Arduino libraries conflict with each other. There is no standard guidance for writing libraries, or even for documenting the resources that a library uses. There is also the problem that the Arduino has few resources so it may not always be possible to avoid conflicts.
If I understand you correctly, you are suggesting a scheme in which a library might be directed to use different pins or different interrupt vectors so that your code could use the pins or vectors that you would like to use.I feel bound to suggest that it would be a lot less trouble if your code were to use the pins or vectors that you might redirect the libraries to.
And, of course, the library source code is included with the Arduino IDE so you are free to make your own version of any library....R
but assume I'd need to download the IDE directly to find the standard library source files