Can I automate CLUSTALO and output alignment sequence identity?
So, as the first reply said, there's sort of multiple questions here.

For filtering things out from a table, I would absolutely use pandas. https://swcarpentry.github.io/python-novice-gapminder/08-data-frames/ Pandas is a way of managing dataframes in python. It looks like what you want from your table is to remove certain rows, if the content of those rows at a certain column matches certain IDs from a list (pathogen IDs). That's the sort of thing the pandas library is good at.

For managing workflows, I use either bash or snakemake. Snakemake is a python thing. It has some advantages, such as being able to start from an intermediary file (for example, if a workflow is "sequences -> multiple alignment -> phylogenetic tree", it can easily start from the multiple alignment). Also deals with branched workflows quite well. Can be easily installed with conda (anaconda is absolutely a lifesaver for bioinformatics work imo). I still use bash for simple workflows, because it's slightly simpler/faster.

For potential filtering - If you want to keep the top hits as they are, but filter the lower-scoring hits based on whether they have a PDB ID or not, I'd personally look into Entrez queries. They're a way of making your search more specific. Here they're shown for WebBlast, but they work quite well for command line blast too. https://www.youtube.com/watch?v=bxx5uaKjMa8