You will have to have some sort of "T" transition piece between your two types of flooring to support expansion fluctuations. If you meticulously install it you can even go inverted "T" even with a floating floor that can be pretty unnoticeable - this is dependent on how long of a meeting point you have too between the two floors.
The thickness does matter in that if the two floors are at different levels (1/4" will be fairly noticeable), then your T transition will slope. The thickness also matters in that you are installing on plywood. There is just no way in the world I would recommend something as thin as 5/16" on plywood. These types of laminate/engineered flooring are meant for commercial or apartment buildings or at the very least a very flat concrete slab. The thinner the flooring material the greater the chance that you feel "air" from the bounce you get on plywood which could lead to issues down the road.
Please refer to my answer here on the specifics of cheaper/thinner flooring -
Low-cost hardwood flooring... what's the catch?
So the only issue I see is if the wood flooring that you are meeting with is pretty low. Too high is fine and you can deal with that with some shingles or felt paper. But if there is a requirement that you need to meet at 3/8", that is going to be hard to deal with. Underlayment will add on at least 1/16" and likely closer to 1/8". Also there is the "air" factor since it is floating floor. You can easily test a small area of flooring and see if you put a heavy box on a floating floor it will go down 1/16" to even 1/4".
To answer your question though, generally thicker is better. You want the thickness to be from rubber/plywood backing not MDF. You want the thickness (don't worry about settling) to be equal to the floor it is meeting.