Based on the advice from Teresa Villena I was able to find a way to solve this issue. Here is the T-SQL code I am using to create each version in case it will help someone else. This creates a private version.
exec sde.create_version 'sde.Default', '{VersionName}', 2, 0 , 'Owners Version';
update data.sde.SDE_versions
set owner = '"{Domain}\{User}"'
where name = '{VersionName}'
The rest of the versioning process must still be done in python to Reconcile, Post and Delete versions followed by killing connections and compressing the states. Does anyone know of a way to compress the states other than a custom script that moves the edits from the delta tables to the base tables?