Some of these conventions are pretty arbitrary and just thought of right now.
When your mod has a naming conflict with another mod, yield if the other mod had that name before you did, or ask the other modder to yield if you had that name before they did.
Yielding for equipment can be done by just placing an @ comment after it, e.g. Generic Sword@genericmod.
Yielding for fighters, skills, remix rules, etc. requires coming up with a new name entirely, or inserting a blank symbol somewhere, e.g. Generic Gadget[]. The blank symbol cannot be seen in-game.
Oooh, this one's tough. Some people _merge properties into existing skills or equipment as to improve how they work with the modder's own items. If multiple modders get the idea to do this for the same skill/equipment, compatibility between those mods will break.
I don't know how to resolve this. I guess if you want to _merge into something someone else has already _merged into, you can just reach out to them and ask them to implement your _merged properties and do vice versa for theirs. This solution only works because the modding community is super small; if it were something like The Binding of Isaac's we'd need some solution incorporated into the game itself.