We do not do that, as
1. we do not have a mechanism/tools to handle it
2. changes made to the environment would not be trackable - right now the installer updates the metadata (even for hotfixes) that allows us to track fixes. With the method you propose, there would be no way to tell for example which fixes will be overwritten by an update, or by a subsequent fix and so on.
3. risk involved - because you would effectively end up with a custom version of the jar (and the whole product) that noone else has tested before (especially after you accumulated more than one fix per jar)

To sum up, I would highly discrecommend considering this approach.

We have been using this fix approach for many years in some very large products in IBM (like WebSphere).  We have tooling to determine the prerequisites, build and package the fix and tooling that takes that metadata into account during install to prevent regressions from overwriting the previous fixes, etc.  However, that tooling was all written for CMVC which is an IBM product that is no longer supported.  I am trying to safely use this same method of support using RTC and cannot find a way to reliably determine the prerequisites.  We cannot change our entire support strategy because we had to move to RTC.

So, I was really looking for someone who is supporting products in RTC using a similar approach to discuss how the managed to determine the prereqs.