I'm not sure I follow completely, but maybe this will help.
Plugins have entry points that the process models call at the appropriate times. These entry points are not model callbacks and they don't override model callbacks.
To call plugin entry points, a process model calls sequences in ModelSupport.seq, such as Model Plugin - Pre UUT. These sequences loop through the list of add-ons and the list of plugins that are configured and call the corresponding entry point in each one. The usual model plugin configuration file is the one the Results Processing dialog box creates at ProgramData\National Instruments\TestStand 2020 (64-bit)\Cfg\ModelPlugins\ResultProcessing.cfg. but there can be more.
Model Plugin - Initialize is always called for plugins in a configuration, to give each plugin a chance to enabled itself if it is disabled. If your model plugin Pre UUT entry point is not begin called, but your Initialize Entry point is, it is probably because it is not set as enabled is the configuration that lists it.