Transparent objects in Illustrator file submission

Hi, sorry if this question seems very basic, but I didn't find any resources somewhere else. Is trasparent objects allowed in ai file submission? I heard that any transparecy in your file can cause rejection. And if this is true what can I do for example, if I have 2 objects, one in front of the other, & want the back object be partially visible. Normally you do it by changing the front object opacity.

Thanks