Have a doubt regarding the Datamart Jobs and SP. Can the store procedures be altered to include custom object tables for reporting purpose ?
Why not if you have the will and skill and are willing to remove your system from support.
Technically that should be too difficult.
Consider consulting or involving CA or CA Service if you want to proceed in order to preserve some controllable supportability.
Please do not make any changes to the existing jobs/procedures.
If you wish to perform datamart type operations on your custom objects data, then currently you would be best off by creating your own jobs and procedures separately, mark the jobs you create as 'incompatible' to the regular datamart (this just prevents them from running at the same time if they are scheduled close together, and makes one of the jobs wait until the other completes), and schedule them to run after you normally expect the datamart jobs to finish.
Modifying the out-of-the-box procedures and/or jobs can not only impact your ability to get support for problems arising with the datamart due to the use of unsupported customizations, but also during any patch or upgrade you risk running into clashes and incompatibilities that will be more difficult to back out / reapply or fix. So separation of the customization from the out-of-the-box procedures is strongly advised.
Retrieving data ...