Hi Jean-François Verdoodt , thank you for this feedback.  It seems that these settings were never extended to the project automation integration.  It seems to be the same for 2024 :-( 
I'll create an API change proposal request and followup with the dev team.  good catch (y)

+Loredana Stoia 

Hi Patrick Andrew Hartnett ,

thanks for your answer. That means that as long the change is not accepted  and developed this cannot be done in any way except user changing it manually ?

Hi Jean-François Verdoodt , I don't have any work arounds for this as it depends on extending these settings from the project automation api.  However, there is nothing stopping you for attempting to access these settings from the internal project via reflection.  I don't recommend this btw and won't provide any support on this, but here is a snippet to get you started if you decide to go down that road. 

var project = new FileBasedProject(projectInfo);
var internalProjectType = typeof(FileBasedProject).GetProperty("InternalProject",
    BindingFlags.NonPublic | BindingFlags.Instance);
var projectInstance = internalProjectType?.GetValue(project);

Hi Jean-François Verdoodt , update from the development team.  They will expose these properties in the public API with the next >= minor release; I don't have a date for this; it will be announced in due course.

Until then, I received this workaround from the team:

The Setting for any SettingGroup can be accessed by string ID too (as long as you know the correct ID)

The Sdl.ProjectAutomation.Settings.AnalysisTaskSettings is just a wrapper that provides a user friendly access to the settings but does the same thing behind the scenes.

As a side note, in the Sudio UI. So ExcludeLockedSegments = true will deactivate the ReportLockedSegmentsSeparately and also set it to false

ISettingsBundle settings = project.GetSettings();
AnalysisTaskSettings projectAnalyseSettings = settings.GetSettingsGroup<AnalysisTaskSettings>();
var excludeLockedSegments = projectAnalyseSettings.GetSetting<bool>("ExcludeLockedSegments");
excludeLockedSegments.Value = true;
project.UpdateSettings(settings);

ISettingsBundle languageSettings = project.GetSettings(new Sdl.Core.Globalization.Language("de-DE"));
AnalysisTaskSettings targetLanguageAnlysisTaskSettings = languageSettings.GetSettingsGroup<AnalysisTaskSettings>();
var excludeLockedSegmentsTL = targetLanguageAnlysisTaskSettings.GetSetting<bool>("ExcludeLockedSegments");
excludeLockedSegmentsTL.Value = false;
var reportLockedSegmentsSeparatelyTL = targetLanguageAnlysisTaskSettings.GetSetting<bool>("ReportLockedSegmentsSeparately");
reportLockedSegmentsSeparatelyTL.Value = true;
project.UpdateSettings(new Sdl.Core.Globalization.Language("de-DE"), languageSettings);