You took your Trans to a reputable shop I can only assume .
That said, they rebuild transmissions on a production scale, I.E. internal build , exterior quick cleaning and a fast rattle can paint to make it presentable.
The builder uses silicone as a matter of speed and not having to deal with stocking or ordering gaskets for everything that goes over his bench.
That said, there is no good reason for not using the gaskets you supplied unless he wasn't handed them at the time of assembly by the front office.
OK so much for the shop not blasting the case and laying on a show quality paint or powder coat job like you would. That would cost extra if they even offered something like that.
The final test is the road test , If it works like new, then your golden. Unfortunately for you that sounds like it will be quite a while before its on the road.
So talk the shop about the gaskets and about the warrantee being extended and get it in writing .
