I actually decided to automate combining the ref assemblied for given CA assembly. Starting from v1.0.19.0 there before packing the assembly Compiler will always analyse all cases of ManagedActions using this assembly and it will always pack the combined set of referenced assemblied. Thus the original code as below will be compiled just fine:
new ManagedAction("ShowDatabaseDialog"), new ManagedAction("InstallDatabase", Return.check, When.Before, Step.InstallFinalize, Condition.Create("&Database_components=3")) { RefAssemblies = new[] { @"files\Sql\redacted.Services.LedDisplay.Sql.dll"} }