Hi Lars,
Thanks as always for your extremely thorough answer, and sorry for my delay in getting back to this post.
I am marking this as the correct answer because I believe that you have 100% correctly answered the question of where the objects go.
There must be some strange security in place on my system where either I cannot see them, or I cannot activate them. After activating a .PROCEDURE file with no activation errors, I execute the SQL: select * from procedures; I can see all procedures in my database except for the ones that were created via .procedure file.
It's weird, but oh well, I just won't use the .procdure files anymore. I have no issues with the .hdbprocedure files. I can see those just fine!
So, thanks for the great answer!