Rape is listed under the Sex & Nudity tab on Parental Advisary

It's a good point. The parental guide pages used to be very user-controlled, but have recently switched to a different format. If IMDb agrees with your point, there could perhaps be a warning message if a contributor uses the word rape, indicating how rape scenes should be described.

I believe it would be best to put "the rape scene" in both sections. 

I avoid placing it in both (preferring only the violence section) unless the rape involves nudity or if the manner of the rape is more akin to date rape (intoxication-involved) or statutory rape than to conventional brute force/intimidation.

Yes, I agree with you. 

@jeorj_euler​  But rape does involve sex. It should be listed in both, I think.

I'm just reporting what I do or try to do, irrespective of what ought to be or what is the best practice. So, yeah, indeed sometimes sexual violence exudes so much sexuality (even if without nudity) that referencing such a scene in the "sex and nudity" category is unavoidable, and forced/coerced sex (usually sexual intercourse) is exactly what rape is.