Unless you are running a very high stall converter, the TruCool 40K is overkill. If you are overheating the trans on a stock converter, there is something else wrong there. Also, the thermal bypass you speak of is basically like a thermostat that gets the trans fluid up to temp quicker in cooler conditions. Hot fluid is just as bad on the trans as cold fluid that runs through like taffy. That's why those coolers come with that option. If this is not a daily driver and you live in a warmer climate, the thermal bypass option is completely unnecessary unless you do a lot of cold winter driving.
What converter do you have? Many times, a smaller stacked plate cooler from your local auto store is plenty sufficient. (think Hayden)