First production run - design PCB for through-hole or surface-mount?
There's no reason to go with through hole. There, I said it.

With a decent microscope, a pair of soldering irons (to lift double sided components), hot air, solder paste and some flux you can easily solder components and modify things. I do 0201 on a daily basis with this setup. 0402, 0603 are no big deal. Also TSSOP, QFNs can be soldered (QFN with flux and hot air is pretty easy).

Through hole forces a completely different architecture for the board layout and the results of using a through hole design could differ, especially as it concerns EMI (think FCC certification). You want your board to resemble as close as possible the final product. Through hole requires space on both sides of the board for the holes and so wastes precious PCB area. Smaller PCB usually means lower emissions too (as well as lower costs etc).

BTW, this doesn't mean the whole design has to be surface mount. 32kHz crystals do come in SMD. There are plenty of them at digikey.

I realize this is an opinion but the reality is SMD isn't the terrible thing that its been made out to be, even for hobbyists.