I personally think the right idea is this:
All design that can be SMD done that way and assembled, with exception of the processor. Or, if the processor is SMD, allow header for connections so it could be desoldered in a hack and the header used for possibly joining multiple boards. Like many, I think this would be a great board to hack into a dual polarity supply or something else.
The users would solder the through hole pieces, LT3080, heatsink, encoders, headers, power jack, etc. (possibly MCU).
This keeps your assembly costs lower (I assume all SMD is much cheaper than SMD plus through hole.) Keeps the kit with non-intimidating pieces. And greatly reduces part count to be put together for the kit.
There is one other thing that I love with the SMD design. I would venture to say that many more people have done work with through hole than SMD. We have a board design that you have done with through hole. It will be cool to see how layout techniques and look changes for SMD. I'm currently learning how to make that change after laying out TH boards for decades and getting into SMD. I would be able to take a look at the SMD board and compare it to previous TH versions and see what needs to be changed, what is harder, what is easier. etc. So the change midstream is actually very instructive.