Tl;dr: the American Health Care Act of 2017 (AHCA) doesn't specifically consider sexual assault a pre-existing condition (PEC), (an unknown amount of) insurance companies consider (the consequences of) sexual assault a PEC. The AHCA only regulates how those companies can treat people with PECs.
This is an emotional and controversial topic. And the answer which will satisfy you will probably come down to semantics (i.e. what does it mean to "allow rape" to be a pre-existing condition? Or what does it mean to "consider sexual assault a pre-existing condition"?).
I'll try to be as comprehensive as I can, but I'll let the reader decide if the answer to this question is a yes or no.
What is a pre-existing condition?
If you read around on the internet, you'll find that there are more than one definition of the term.
One Wikipedia article describes a PEC as such:
The University of Pittsburgh Medical Center defines a pre-existing condition as a "medical condition that occurred before a program of health benefits went into effect"
Something along these lines is most likely the definition a health care insurance provider would use. However, there are others who use PEC to describe a type of loophole used by insurance companies. To quote the OP:
[PECs are] reasons for an insurer to deny insuring you, or ask for a higher fee.
Or take a look at this article from Politifact: Obamacare to stop domestic violence as pre-existing condition. This is also a good example of people using the term PEC to refer to a "loophole".
To make this answer valid for this site I'll use "the most scientific" definition (IMHO). So from here on out, a PEC is considered a medical condition that occurred before a program of health benefits went into effect.
Obamacare and PECs:
If you have the "correct" definition of a PEC in mind than those articles listed in the question are somewhat misleading. As an example, consider this one snippet from the Independant:
Before Obamacare, some insurance companies considered rape and domestic abuse pre-existing conditions.
They still do. Obamacare only regulated how insurance companies can treat people with a (certain) PEC. As a matter of fact, the Patient Protection Affordable Care Act pretty much says that domestic violence is a PEC:
SEC. 2705. PROHIBITING DISCRIMINATION AGAINST INDIVIDUAL PARTICIPANTS AND BENEFICIARIES BASED ON HEALTH STATUS.
(a) IN GENERAL. — A group health plan and a health insurance issuer offering group or individual health insurance coverage may
not establish rules for eligibility (including continued eligibility)
of any individual to enroll under the terms of the plan or coverage based on any of the following health status-related factors in relation to the individual or a dependent of the individual:
(7) Evidence of insurability (including conditions arising
out of acts of domestic violence).
American Health Care Act of 2017 (AHCA) and PECs:
The AHCA follows the same style as Obamacare, i.e. it doesn't contain a comprehensive list of "acceptable" PECs. It does however (de)regulate how insurance companies can treat them.
Politico.com explains the differences between Obamacare and the AHCA:
[The insurance companies] have to provide access to coverage for people with pre-existing conditions. It says nothing about the rates of that coverage.
That means if the AHCA passes, it would allow for people with pre-existing conditions to be charged more per year for their insurance coverage – possibly to the tune of thousands or even tens of thousands of dollars more per year, some studies have found.
So people can not be denied coverage, but theoretically they can be charged extra to the point that some can't afford it.
Health care insurance companies see a PEC as a medical condition that a person has before or while getting a health insurance. Before Obamacare this meant that they could deny service or charge extra. Obamacare made it harder for insurance companies to do this. The AHCA made it again possible that these companies can charge extra.