NMRog
For liability reasons TC has to install the barrel - tang - trigger & lock into the new stock. They will honor your warranty even with the alterations to the stock.
Think I would call TC direct - they will transfer you to the shop... tell them exactly what you have written here + you want the old stock back with you ornamentation. The other option is to tell them about the ornamentation and that you are going to remove it prior to mailing it all in, and because of this the stock will have voids in it.
The last option is toship the assembly certified and insured to TC and request they ship it back the same way.
I still think the best bet is to call them again and discuss your concerns and see if they can suggest possible options.
Hope something works for you. TC has down some warranty work for me in the past and were A1.