I duplicated and wrote up your issues 1 and 3. If you want to be notified when it is fixed please
send an email via the 'Contact Support' link and include "Notify Me When HMT-5914 Is Resolved" in the subject line and body of the email.
I was not able to duplicate the issue you mention for number 2 with the IsOmahaWrap3Wrap0Gap = true filter as you can see in the attached image. I believe that filter is working as intended for me with this old sample of my PLO hands.
hm3 wpn omaha holecards - 3 card wrap zero gap.png