Alright, after some digging through workarea files (answer was in \Workarea\controls\content\UrlAliasing\editAliasesTab.ascx.cs), the current approach uses a frameworkAPI manager object in the namespace Ektron.Cms.Framework.Settings.UrlAliasing
This object appears to be able to handle both manual and automatic aliases, although its standard "get" methods only return automatic aliases in my testing, and the getDefaultAlias method always returns an empty string. The manager does work as expected, returning all associated aliases, when using the Alias Criteria objects located in 'Ektron.Cms.Settings.UrlAliasing.DataObjects.AliasCriteria'. Objects returned are generic to alias type, and will indicate if they are a default with the isDefault property.
The following will pull out all aliases regardless of type:
Ektron.Cms.Framework.Settings.UrlAliasing.AliasManager aCRUD = new ektron.Cms.Framework.Settings.UrlAliasing.AliasManager();
Ektron.Cms.Settings.UrlAliasing.DataObjects.AliasCriteria aSelector = new Ektron.Cms.Settings.UrlAliasing.DataObjects.AliasCriteria();
aSelector.AddFilter(Ektron.Cms.Settings.UrlAliasing.DataObjects.AliasProperty.TargetId, Ektron.Cms.Common.CriteriaFilterOperator.EqualTo, contentId);
var allAlias = aCRUD.GetList(aSelector);