After Tax Safe Harbor

Plan is Safe Harbor match with a discretionary match and after tax option.  If the plan does not put in a discretionary match and employees decide to put in a 4% after tax contribution, does this need to be tested under ACP or can it be avoided?

Yes. After tax contributions are tested under ACP, being a Safe-Harbor Plan does not get you a free pass on voluntary after-tax contributions.

You may also run a foul of the free pass on Safe-Harbor exemption, if that is a potential concern, but I'm not sure about that one.

after tax has to have ACP testing 1.401(m)-3(j)(6)

you can use the safe harbor match in ACP testing as well.

1.401(m)-2(a)(5)(iv) permits you to exclude matching contributions that do not exceed 4% of comp.

general consensus is top-heavy free means nothing other than deferral or safe harbor so that is probably ruined.

I just looked at the Code, hoping that it would say something like a plan where "the only EMPLOYER contributions are...." but it doesn't say that. 

(Meaning, EMPLOYEE contributions might have been a loophole.  But, apparently not, indeed.)