I disagree on the repertoire for ATCL/Dip (having done both myself) - I found them very similar. In the light of your comments, I am a bit bemused by your suggested programme because Litanies is on the LRSM list and the Variations are on the LTCL list!
For info, at ATCL I did Buxtehude BuxWV159, Hindemith Sonata III, Bairstow Organ Sonata 3rd movt and Rheinberger Sonata 12, 1st movement.
Remember you will need to seek approval from the Trinity dip office for your own choice programme. This is not necessary if you choose off their list of course.
For organ specifically, I don't think it makes much difference whether you have ATCL or DipABRSM, they are both good achievements - especially for a 16 year old. Have you considered starting the RCO diplomas, perhaps the CertRCO, which if you like are the "industry" standard for organists? What does your teacher think?
That aside, you can certainly do the ATCL at your choice of venue, you make the arrangements through the local rep. It is nice to be in control of the venue and to know the instrument well. One less thing to worry about on the day!
Good luck! Take a look in Viva Organ as well since we often discuss diploma matters therein too.