When using a portal feature service for a table and a feature, joining them via uniqueid (guid 38) the feature joiner fails to join even though the guid is value. The dataset is branch versioned. Am I missing something?

Hard to say, can you inspect both datasets before joining and confirm the guid's really match?

After comparing uniqueids within portal of a table against a feature, changing the workspace>translation>rejected feature handling of feature joiner to continue translation instead of terminate translation allowed the tool to work as expected. Apologies I did not catch this before.