Can I use 1/2" rough-in for the thermostatic valve with 3/4" rough-in for the transfer valve? These are Kohler products and the transfer valve rough-in comes only in 3/4" size.
Thank you.

Can you explain why you are not using 3/4 for everything? Which Kohler valves are you using? The install manual tells you the size of the supply pipes, what's yours say?

If you are planning on installing only 1 shower head on this mixing valve than you should not worry about it.

Before purchasing the shower, I asked the plumber if I should get 1/2" or 3/4" rough-in. He said 1/2". And that's what I got for the thermostatic valve, but i did not have the option for the diverter/transfer valve. I purchased the 3/4" transfer rough-in without speaking to the plumber first. I want to install a hand shower in addition to the regular shower. I am hoping there is something that will allow to connect both rough-ins.

Thank you

It happens all the time...
Plumber will have to use reducers to reduce the diverter to 1/2" on both ends. He can use copper or brass fittings to do so. It is a bit more work for him - but certainly not a reason to return the valve.

You should be fine with 2 shower head outlets as long as they have Low Flow restrictors installed - as it is mandated by the Code.