There is an issue with postprocess script, where shell script build phase is edited manually:

if (section == "PBXShellScriptBuildPhase" && line.Trim().StartsWith("shellScript"))
{
pbxproj.Flush();
pbxproj.BaseStream.Seek(-2L - Environment.NewLine.Length, SeekOrigin.Current);
pbxproj.WriteLine("\\necho \\\"Hello\\\"\";");
}

What is happening, is that we add shell script in GameAssembly to run il2cpp build.
Now, we really need il2cpp build properly done, so we always add this run script phase with proper commandline etc.
This works in both replace and append, since internally (in PBXProject) when adding shellscript phase, we are checking first if such phase exists already (by comparing name/commandline/some other things), see https://docs.unity3d.com/ScriptReference/iOS.Xcode.PBXProject.AddShellScriptBuildPhase.html
Since pbxproject *text* itself is edited, when we load it to append, the buildphase that GameAssembly needs is different from what is in the project, so it is added anew. And mind you we cannot just delete previous one because this is, kinda, no longer "unity added it and controls it"