I really do not know the answer to if it would ruin the seals,
I honestly would not waste my time and money on the product.
I knew better, but a guy on craigs list had a 5 gallon pail of it for $10. What the heck, I need 2 gallons and with 5 I can put on 2 coats. In 6 months the product is just gone and I need to redo it again. Is simply a small garden shed in my yard with stain grade T1-11.
I just regret using it in the first place.
I have many jobs out there, including a garden shed for a friend. I used sikkens on it and at 5 years old, would not even consider it time to redo it. I have many other projects running 6-7 years in the New Mexico sun and look great.
I pay $65 per gallon for sikkens, they have two quality levels and the flat finish is the cheap one, I do not use it.
Another product I will use is penofin. It is more reasonable at $35 per gallon, I buy a lot of rough sawn lumber, corbels, beams, columns and is what that store recommends.
Is also easer to find in my case.
I use a pump up sprayer to apply, but really am sorry you are using Thompsons water seal, should just be called Thompsons water.