The short answer is yes different skeletons can share the same animations and blueprints but does take planing and requires following some simple rules
Follow the examples the base hierarchy “has” to be the same but children can be added as to functionality, say adding a duster jacket, and will accept animations as to the additional bones.
Where the depends comes in is in the purpose that needs to be served, with in context, and in general the answer is usually no with out knowing the relative positions and references being made to the additional skeletal assets.
**For clarity targeting = transferring key frame data from one rig to another that shares the same structure and naming convention as to references. Re-targeting = transferring key frame data from one rig to another that does not share the same naming convention as to references. **
A good example of this practice in use is the Paragon examples that shares the same base Epic rig, that at one point shared the same base hierarchy, but with each character requiring additional bones to accommodate unique requirements like weapons and such. You can test this in theory by by setting up a 3rd person template, add the Paragon character to project, and then change the skeletal reference to the 3rd person version. The targeting to the new reference will take place but UE4 will respond that there are additional bones required and if you want to included them.
Do the same process to all of the Paragon assets and you will now have over 3000 animation assets targeted to the base third person rig, along with unique requirements, back to what I would assume is Paragon’s original character model structure.
Some notes on the auto-rig.
An interesting feature addition but I’m hard press to see any situation where such level of control is required. The idea of animating in UE4 for the purpose of game play seems rather redundant consider there are far better tools for the purpose of authoring animations that equals the same level of learning to build a rigging system to drive a single need purpose. My weapon of choice for example is Motionbuilder so tasks like targeting and re-targeting is a task best done over a cup of coffee and and donuts as this is a key feature of MB as to the need.
Once a character in MB is characterized MB becomes object aware that the character in hand is a biped character so access to and activation of tool sets available to such an object becomes activated, including a “Control Rig” that can be used to drive all of the animations, so I’m thinking Epic is in the process of a system where a single channel system could be applied, as a one rig to serve them all, that will forgo the need to re-target in the first place.
Just some thoughts.