The example, Section V.B.1.a., and Section V.B.2. all state that safeharbor contributions must be made on behalf of each NHCE who is an eligible employee.
There are at least two ways to demonstrate that this precludes a 1,000 requirement. First, the 1,000 hour requirement mentioned in your facts is, literally, only an allocation requirement, not an eligibility requirement. The imposition of this allocation requirement would mean that safeharbor contributions were not going to all eligible employees. Second, although it is tempting to think of matching contributions as a seperate "plan" for purposes of these safeharbor provisions, they are not. Section IV.A. provides that the 1.401(k)-1(g)(11) definition of "plan" applies. 1.401(k)-1(g)(11)(ii) provides that (k) and (m) components are not mandatorily disaggregated for these purposes.
Although V.B.3.Ex.4 does not mention a 1,000 year requirement as violating the safeharbor requirements, it clearly is precluded.