The client searches folders in this order:
fs_homepath/fs_game
fs_basepath/fs_game
fs_homepath/base
fs_basepath/base
Within those folders it searches in reverse alphabetical order, and uses the first files it comes across. So if you want your pk3 to be recognised, it will have to either be in your home directory or after data-1.1.0.pk3 alphabetically (e.g. data-1.1.1.pk3 or MMD-uniforms.pk3
It's not necessary to replace the whole pk3, because the client can derive its data from several pk3s. So long as the file is where it is expected to be in the pk3 it will be found (e.g. you could have just models/buildables/arm/arm_body.jpg in your zip and only that file would be overridden)
is there a way it can be on the pure check allow list, but not required for download?
I've had the same idea but I can't think of a way. Perhaps it will be a modding project for me (or someone else): optionalpaks.dat, referencing files on the server that clients are not dropped for missing but are not forced to download. They can still be checksummed to avoid cheaters, but those without can play anyway.
edit: to get your current running mod, read /fs_game in the console. To start up in a mod, run from the command line with +set fs_game mod.