I think the point is that those are not loans into English, rather they are international scientific terms in terminology that is used by many people whose firs

I think the point is that those are not loans into English, rather they are international scientific terms in terminology that is used by many people whose first language is neither English, nor Latin (or Greek). So there is no reason to have a convention that is specific to English, or any other language, besides the Greek or Latin of the original. In essence, when you use a word like "amygdala", you are not using English. Rather, you are code-switching between Latin and English.