The amd64 version is (mostly) for a select few mods with memory exhaustion problems. If your mod doesn't have this problem then there is no need to use the amd64 version.
No-pe. I would make each an archive with the specific weidu tacked along. It's more work ... well, one could automate this with a windows script that takes a modname as a variable and a mod folder, and thus makes the different archives automatically. But even as I am not a programmer that can do that, I know it's possible. PS, there's already one .. for G3 mods.
We now have x32 and amd64 versions of WeiDU. We still have autoupdate and packaging that uses setup-mymod.exe
What is considered best distribution practice for this situation?
I can see running a batch filke that querys the OS and renames one of two weidu.exe. Or have manual instructions to rename the correct file to setupo-mymod.exe. Or i could see not distributing weidu at all (shuppoing a folder with a .tp2 inside and requiring a user to rename or download and rename their needed version.