I have replaced a few trims in my day.
Not on a custom tank but average aqueon/perfecto/odell(remember when...)
The trims/frame can be replaced without effecting the integrity of the glass to glass seal IMO
I can't even say for sure the trims aren't added after the glass has been sealed and cured.
I would look for a couple bucks back if you are really worried.
You are correct in thinking they only need to worry till end of warranty which doesn't cover much agreed!
I don't think the work they are doing should have any effect on tank seal.
Hope this helps ease your mind Harry.