OK, that's imperfect world and we suffer.
1) There is system bus order, how your motherboard PCI bus enumerates cards. These are numbers like "03:00:00" "1a:00:00" and so on. It's a PCI bus id.
IT HAS NO RELATION TO PHYSICAL ORDER.
Though 16x slot card might be always "01:00:00". But when you remove let's say 3rd card then others order may all messed up again. Be careful when you have separate OC settings for this.
2) Miners access GPUs not directly by the system interface. The use let's say APIs. OpenCL for AMD and CUDA for Nvidia. And surprise-surprise they have their own order based on the drug doze of their respectful developers. And again IT HAS NO RELATION PHYSICAL ORDER.
3) Some miners are so smart so they mess even this worth situation and introduce their own order.
So how do I find where is my physical GPU on the system?
Easy. Set manual fans. For example 100% to one GPU and 20% for others. You will notice the difference)
Or set "-di 3" in claymore settings to mine only on 3rd GPU for example.
For Nvidias PCI bus and CUDA order are the same now. But still physical order is unpredictable.