JEM models only allow to use textures in a vanilla namespace (in "minecraft" folder),
use any other namespace (custom:textures/entity/...) causes an error.

I think it should work simularly to item/block models:

• "textures/item/stick" - Has no namespace so it will use vanilla namespace
• "custom:item/pebbles" - Has different namespace, will use "custom/textures/item/pebbles" texture, "textures" folder can be ignored in path because there is namespace (yes, it works like that in vanilla)

In my resource pack, I placed all textures and item models in a separate namespace in order to place them separately from vanilla assets and shorten path to textures.

I didn't notice some lines in the logs, it was a mistake of another mod which did not take into account this and caused a resource pack error

+1 for that! :)

to work with random it should be possible to do it in the .propertie too tho.

the ability to specify a full path instead of a simple suffix
ex:

skins.2=custom:my_mobs/texture_2
name.2=iregex:blabla

what error does using a namespaced texture give you, it should work fine?

as for sebs suggestions it would be nice but break optifine compat needlessly

(yes, it works like that in vanilla)

no it doesn't.
yes that is a thing for block models, but that is not at all a normal resource declaration, and not all mods have their textures pathed correctly

jem models require the textures/ part
I suggest you read this

I'm happy to consider expansions on the above listed supported options but changing these will needlessly break optifine compat