PseudoLMGenerator is a tool to generate a “landmark template” that will be used across a study. If you change the reference specimen that you use with the PseudoLMGenerator, you will not get the same set of landmarks. So it is important to use a specimen that will be representative of population, or even generate a sample average (so that the template is not bias against/for any of the specimens). See the tutorial at https://github.com/SlicerMorph/Tutorials/tree/main/PseudoLMGenerator
You will need a tool like ALPACA or a set of fixed LMs to transfer this template to target samples.
So, in short you cannot generate pseudoLMs for every specimen, and run an analysis on them, since the number of landmarks and their placement will be different. You can try placeSemiLMPatches module for that. However, you should have a set of fixed LM to be able to use that tool.