It has been years since I did some testing in the DO-160 cage, but as I recall here are the answers I would give you:
The DC ripple test is to make sure that ANY equipment installed does not internally generate and impose ripple on the power distribution system greater than the test limits specify. The type of equipment is immaterial. In other words it is not limitied to power generatiing equipment only. Any equipment installed on the power distribution system is not allowed to introduce ripple onto the power distribution system in excess of the limits, and the purpose is to protect all other units installed on the power distribution system as well as protect the power distribution system itself.
There is no need to isolate the ripple coming from the internals of the unit under test when performing the AF test. Whatever ripple exists from inside the unit under test is already there and considered to be the normal working environment of the unit under test. You set the externally introduced ripple energy to the specified levels and apply it. What the power input lines of the unit under test will be experiencing is the externally introduced AF plus the internally generated ripple, which is the "real world" scenario that you want to test.
For example lets say the unit under test has an internally generated ripple of x. Then when you perform the AF test, assume that you are instructed to externally introduce AF at a magnitude of y. During the AF test the power line with the externally introduced and internally generated ripple will experience total ripple/AF energy of x + y. For the purpose of this illustration I am ignoring phase and frequency but in real life the waveforms will not add in a linear manner unless your test setup sychronizes both phase and frequency.