It seems like several mods break when you set items to be non-stackable.

Which mods specifically? Non-stackable items are a thing in vanilla (e.g. the artillery shell), so if any mods can't handle them it's their problem.

248k, and Omnicompression are the two I found. While they are technically a thing in vanilla, that flag is allocated only to the selection-tool, copy-paste-tool, cut-paste-tool, and blueprint prototypes as far as I can tell. 248k fixed it on their end, but Omnicompression hasn't.

No idea why I even put the non-stackable flag there in the first place, fixed in 1.6.3.

You probably though that you had to set it if you also set the stack size to 1.