This is a pretty grey area in terms of getting points allocated for CRS. Incorporation is only for tax purpose hence only CRA(Canada Reveneu Agency) is involved.
BIG difference : All Self-Employed individuals are incorporated, NOT all incorporated individuals are self-employed.
CEC does not allocate points towards self-employed individuals as it's hard to find out the exact number of working hours. In such cases self-employed individuals generally work under professions of farming, taxi driver, athletes etc... where an individual can work any number of hours and does not have an employer-employee relationship.
In my case, even though I am incorporated, I am an IT consultant and I have a NOC 2171 and I have a strict 9-5 job with specific roles & responsibilities defined by my employer and I work at my employers location. Only for the purpose of CRA and filing taxes I am considered otherwise I am not, hence by the clear definition of HRSDC (Human Resources Development Canada) I do NOT title myself as self-employed. Hence, I did not check mark either OOPNP or EE submission as self-employed. I submitted as regular employment and have provided all supporting documentation.
If for some reason CIC or OOPNP comes back to me saying its self-employed I can counter argue with the HRSDC document of employer-employee relationship. Even if then they deny me then I am still above the 400 mark.
I haven't received my PNP nomination yet, so I cannot tell you whether they accepted or not. You can look up HRSDC website and read about it and submit it at your own risk. I am not suggesting anything here as to what you should do, except just sharing my part.
Hope you have a better clarification than before.