It is VERY difficult to get the trim out of the clips without bending it. A really good installer may be able to accomplish this, but I guarantee they’ll have new trim on-hand in case the existing parts get tweaked.
Personally if they absolutely refuse, I’d do an extremely close inspection when they give it back to you and if it isn’t as smooth and straight as stock at that point I’d insist on replacement.
The other thing they often do is use urethane to anchor the stainless clip at the top because they already have a bunch of it on hand. Toyota calls for a flexible epoxy, and I’m sure they have their reasons.
Very helpful! They haven't refused anything at this point, but when I asked if we needed to order any additional parts they said no and explained that everything was reusable minus the clips. You're right about the urethane; they have a $30 line item for "Adhesive (Fast-Cure Urethane/Dam/Primer). I will reach back out to them and see if they can update the claim to include the seals and mouldings. If not, I'm happy to provide at my expense.